[R/AllClasses.R:1:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L1) *style:* **Variable or function name should be snake_case.**
```r
validateS4 <- function(...) {
^~~~~~~~~~
```
[R/AllClasses.R:66:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L70) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink <- slot(object, "lfcShrink")
        ^~~~~~~~~
```
[R/AllClasses.R:71:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:76:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L76) *style:* **Commented code should be removed.**
```r
        #         y = colnames(rowData(data))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/AllClasses.R:79:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:166:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L166) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(results)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/AllClasses.R:167:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:173:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L173) *style:* **Variable or function name should be snake_case.**
```r
        degMatch <- removeNA(str_match(
        ^~~~~~~~
```
[R/AllClasses.R:177:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/alphaSummary-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L45) *warning:* **no visible global function definition for ‘assert_is_numeric’**
```r
        assert_is_numeric(alpha)
        ^~~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L46) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(contrast, c("character", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L47) *warning:* **no visible global function definition for ‘assertIsStringOrNULL’**
```r
        assertIsStringOrNULL(name)
        ^~~~~~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:61:24:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L61) *warning:* **no visible global function definition for ‘resultsNames’**
```r
            caption <- resultsNames(object)[[1L]]
                       ^~~~~~~~~~~~
```
[R/contrastName-methods.R:29:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/contrastName-methods.R#L29) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        contrast <- mcols(object)[2L, "description"]
                    ^~~~~
```
[R/contrastName-methods.R:30:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/contrastName-methods.R#L30) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(contrast)
        ^~~~~~~~~~~~~~~~~~~
```
[R/contrastName-methods.R:74:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/contrastName-methods.R#L74) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrastName(slot(object, name = "results"))
        ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:5:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L5) *style:* **Variable or function name should be snake_case.**
```r
.addIsDECol <- function(
^~~~~~~~~~~
```
[R/DESeq2-internal.R:7:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L7) *style:* **Variable or function name should be snake_case.**
```r
    testCol = "padj",
    ^~~~~~~
```
[R/DESeq2-internal.R:9:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L9) *style:* **Variable or function name should be snake_case.**
```r
    lfcCol = "log2FoldChange",
    ^~~~~~
```
[R/DESeq2-internal.R:10:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L10) *style:* **Variable or function name should be snake_case.**
```r
    lfcThreshold = 0L
    ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:16:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L16) *style:* **Variable or function name should be snake_case.**
```r
    isDE <- mapply(
    ^~~~
```
[R/DESeq2-internal.R:36:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L36) *style:* **Variable or function name should be snake_case.**
```r
    isDE <- as.factor(isDE)
    ^~~~
```
[R/DESeq2-internal.R:43:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
.ddsMsg <- function() {
^~~~~~~
```
[R/DESeq2-internal.R:58:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L58) *style:* **Variable or function name should be snake_case.**
```r
    lfcThreshold = NULL,
    ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:61:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L61) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:63:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L63) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeq2-internal.R:65:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L65) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
    assertIsAlpha(alpha)
    ^~~~~~~~~~~~~
```
[R/DESeq2-internal.R:67:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:67:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L67) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeq2-internal.R:69:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L69) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
    assert_is_a_number(lfcThreshold)
    ^~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:70:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L70) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
    assert_all_are_non_negative(lfcThreshold)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:74:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L74) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
    padj <- sym("padj")
            ^~~
```
[R/DESeq2-internal.R:75:12:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L75) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
    lfc <- sym("log2FoldChange")
           ^~~
```
[R/DESeq2-internal.R:80:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L80) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset(cols, colnames(data))
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:81:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L81) *warning:* **no visible global function definition for ‘select’**
```r
    data <- select(data, !!!syms(cols))
            ^~~~~~
```
[R/DESeq2-internal.R:81:29:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L81) *warning:* **no visible global function definition for ‘syms’, Did you mean 'sum'?**
```r
    data <- select(data, !!!syms(cols))
                            ^~~~
```
[R/DESeq2-internal.R:101:12:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L101) *warning:* **no visible global function definition for ‘pull’, Did you mean 'poly'?**
```r
    deg <- pull(data, "rowname")
           ^~~~
```
[R/DESeq2-internal.R:108:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L108) *style:* **Variable or function name should be snake_case.**
```r
.matchResults <- function(
^~~~~~~~~~~~~
```
[R/DESeq2-internal.R:111:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    lfcShrink = FALSE
    ^~~~~~~~~
```
[R/DESeq2-internal.R:113:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L113) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqAnalysis")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:118:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L118) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
    assert_is_scalar(results)
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:119:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L119) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
    assert_is_a_bool(lfcShrink)
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:121:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L121) *style:* **Variable or function name should be snake_case.**
```r
        slotName <- "lfcShrink"
        ^~~~~~~~
```
[R/DESeq2-internal.R:123:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L123) *style:* **Variable or function name should be snake_case.**
```r
        slotName <- "results"
        ^~~~~~~~
```
[R/DESeq2-internal.R:126:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L126) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(results, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:129:35:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L129) *warning:* **no visible global function definition for ‘contrastName’**
```r
    msg <- paste("DESeqResults:", contrastName(results))
                                  ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:140:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L140) *style:* **Variable or function name should be snake_case.**
```r
.transformCountsAxisLabel <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:141:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L141) *warning:* **no visible global function definition for ‘.transformType’**
```r
    paste(.transformType(object), "counts (log2)")
          ^~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:146:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L146) *style:* **Variable or function name should be snake_case.**
```r
.transformType <- function(object) {
^~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:147:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L147) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqTransform")
    ^~~~~~~~~~~~~~~~
```
[R/DESeqAnalysis.R:35:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqAnalysis.R#L35) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink
        ^~~~~~~~~
```
[R/DESeqAnalysis.R:48:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqAnalysis.R#L48) *style:* **Variable or function name should be snake_case.**
```r
.contrastNames <- function(object) {
^~~~~~~~~~~~~~
```
[R/DESeqAnalysis.R:49:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqAnalysis.R#L49) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqAnalysis"))
    ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:59:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L59) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResults"))
        ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:60:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L60) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(c("log2FoldChange", "padj"), colnames(object))
        ^~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:61:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L61) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:62:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L62) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:63:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L63) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:63:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L63) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:64:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L64) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:65:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L65) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L68) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/DESeqResultsTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L69) *style:* **Variable or function name should be snake_case.**
```r
        testCol <- "padj"
        ^~~~~~~
```
[R/DESeqResultsTables-methods.R:70:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L70) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        lfc <- sym(lfcCol)
               ^~~
```
[R/DESeqResultsTables-methods.R:71:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L71) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        test <- sym(testCol)
                ^~~
```
[R/DESeqResultsTables-methods.R:120:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L120) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:149:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L149) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- rowRanges(data)
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:159:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L159) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
        mcols(rowRanges) <- mcols
        ^~~~~
```
[R/DESeqResultsTables-methods.R:160:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L160) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
        assert_is_non_empty(rowRanges)
        ^~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:177:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L177) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- sampleNames(data)
        ^~~~~~~~~~~
```
[R/export-methods.R:28:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L28) *style:* **Variable or function name should be snake_case.**
```r
.prepareDESeqResults <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:30:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    rowData = NULL,
    ^~~~~~~
```
[R/export-methods.R:32:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L32) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames = NULL
    ^~~~~~~~~~~
```
[R/export-methods.R:34:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L34) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:35:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L35) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(rowData, c("DataFrame", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:36:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L36) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(counts, c("matrix", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:37:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L37) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(sampleNames, c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L45) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(rowData, "DataFrame")
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L46) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- sanitizeRowData(rowData)
        ^~~~~~~
```
[R/export-methods.R:46:20:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L46) *warning:* **no visible global function definition for ‘sanitizeRowData’**
```r
        rowData <- sanitizeRowData(rowData)
                   ^~~~~~~~~~~~~~~
```
[R/export-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L47) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(rowData))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:54:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L54) *warning:* **no visible global function definition for ‘assert_is_matrix’**
```r
        assert_is_matrix(counts)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:55:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L55) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:62:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L62) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
            assert_has_names(sampleNames)
            ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:63:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L63) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
            assert_are_identical(names(sampleNames), colnames(counts))
            ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:66:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L66) *warning:* **no visible global function definition for ‘assert_are_disjoint_sets’**
```r
        assert_are_disjoint_sets(colnames(data), colnames(counts))
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:75:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L75) *style:* **Variable or function name should be snake_case.**
```r
.prepareResultsTablesList <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:76:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L76) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqResultsTables"))
    ^~~~~~~~~~~
```
[R/export-methods.R:80:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L80) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
    assert_is_list(deg)
    ^~~~~~~~~~~~~~
```
[R/export-methods.R:81:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L81) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(names(deg), c("up", "down"))
    ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:89:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L89) *style:* **Variable or function name should be snake_case.**
```r
    rowData <- slot(object, "rowRanges") %>%
    ^~~~~~~
```
[R/export-methods.R:94:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L94) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames <- slot(object, "sampleNames")
    ^~~~~~~~~~~
```
[R/export-methods.R:102:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L102) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(all, "DataFrame"))
    ^~~~~~~~~~~
```
[R/export-methods.R:117:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L117) *warning:* **no visible global function definition for ‘initDir’**
```r
        dir <- initDir(dir)
               ^~~~~~~
```
[R/export-methods.R:118:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L118) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(compress)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:121:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L121) *warning:* **no visible global function definition for ‘.prepareResultsTablesList’**
```r
        tables <- .prepareResultsTablesList(x)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:122:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L122) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(tables)
        ^~~~~~~~~~~~~~
```
[R/export-methods.R:129:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L129) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        stem <- snake(contrastName(x))
                ^~~~~
```
[R/export-methods.R:129:23:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L129) *warning:* **no visible global function definition for ‘contrastName’**
```r
        stem <- snake(contrastName(x))
                      ^~~~~~~~~~~~
```
[R/export-methods.R:135:51:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L135) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        files <- file.path(dir, paste0(stem, "_", snake(names(tables)), ext))
                                                  ^~~~~
```
[R/export-methods.R:144:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L144) *warning:* **no visible global function definition for ‘export’**
```r
                export(x = x, file = file)
                ^~~~~~
```
[R/export-methods.R:151:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L151) *warning:* **no visible global function definition for ‘assert_all_are_existing_files’**
```r
        assert_all_are_existing_files(files)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/markdown-methods.R:26:14:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L26) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        show(markdownHeader("Contrast names"))
             ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:27:14:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L27) *warning:* **no visible global function definition for ‘markdownList’**
```r
        show(markdownList(.contrastNames(object)))
             ^~~~~~~~~~~~
```
[R/markdown-methods.R:27:27:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L27) *warning:* **no visible global function definition for ‘.contrastNames’**
```r
        show(markdownList(.contrastNames(object)))
                          ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L45) *style:* **Variable or function name should be snake_case.**
```r
        headerLevel = 2L
        ^~~~~~~~~~~
```
[R/markdown-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L47) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResultsTables"))
        ^~~~~~~~~~~
```
[R/markdown-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L49) *warning:* **no visible global function definition for ‘assertIsHeaderLevel’**
```r
        assertIsHeaderLevel(headerLevel)
        ^~~~~~~~~~~~~~~~~~~
```
[R/markdown-methods.R:50:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:54:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L54) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(object)
                    ^~~~~~~~~~~~
```
[R/markdown-methods.R:55:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L55) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        markdownHeader(contrast, level = headerLevel, asis = TRUE)
        ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:56:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L56) *style:* **Variable or function name should be snake_case.**
```r
        headerLevel <- headerLevel + 1L
        ^~~~~~~~~~~
```
[R/markdown-methods.R:57:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:82:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L82) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
            markdownHeader("File downloads", level = headerLevel, asis = TRUE)
            ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:109:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:111:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L111) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        markdownHeader("Top tables", level = headerLevel, asis = TRUE)
        ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:112:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L112) *warning:* **no visible global function definition for ‘topTables’**
```r
        topTables(object)
        ^~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:36:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L36) *style:* **Variable or function name should be snake_case.**
```r
        clusteringMethod = "ward.D2",
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:40:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L40) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(object, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:42:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L42) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(counts, "DESeqTransform")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:44:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L44) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:45:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L45) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotDEGHeatmap-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L46) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L47) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:47:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L47) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotDEGHeatmap-methods.R:48:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L48) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L49) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:51:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L51) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(clusteringMethod)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:37:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L37) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(object, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:39:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L39) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(counts, "DESeqTransform")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:41:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L41) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:42:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L42) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L46) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(counts) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:47:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L47) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotDEGPCA-methods.R:48:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L48) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L49) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:49:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L49) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotDEGPCA-methods.R:50:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L50) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:51:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L51) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:85:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L85) *style:* **Trailing whitespace is superfluous.**
```r
    f = "plotPCA",
                  ^
```
[R/plotDEGPCA-methods.R:108:20:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L108) *warning:* **no visible global function definition for ‘.matchResults’**
```r
        results <- .matchResults(object = object, results = results)
                   ^~~~~~~~~~~~~
```
[R/plotGene-methods.R:32:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotGene-methods.R#L32) *style:* **Variable or function name should be snake_case.**
```r
            countsAxisLabel <- "rlog counts (log2)"
            ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:34:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotGene-methods.R#L34) *style:* **Variable or function name should be snake_case.**
```r
            countsAxisLabel <- "vst counts (log2)"
            ^~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:72:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L72) *style:* **Variable or function name should be snake_case.**
```r
        pointColor = "gray50",
        ^~~~~~~~~~
```
[R/plotMA-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        sigPointColor = c(upregulated = "purple", downregulated = "orange"),
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:77:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L77) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotMA-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L78) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotMA-methods.R:79:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L79) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotMA-methods.R:80:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L80) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:81:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L81) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:82:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L82) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(genes, c("character", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:83:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L83) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(gene2symbol, c("Gene2Symbol", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:85:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L85) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(ntop)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:86:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L86) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(ntop)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:90:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L90) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(pointColor)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:91:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L91) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(sigPointColor)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:93:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L93) *style:* **Variable or function name should be snake_case.**
```r
            sigPointColor <- c(
            ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:98:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L98) *warning:* **no visible global function definition for ‘assert_is_of_length’**
```r
        assert_is_of_length(sigPointColor, n = 2L)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:103:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L103) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "svalue"  # nocov
            ^~~~~~~
```
[R/plotMA-methods.R:105:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L105) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "padj"
            ^~~~~~~
```
[R/plotMA-methods.R:109:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L109) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/plotMA-methods.R:140:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L140) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) > 0L)
                                   ^~~
```
[R/plotMA-methods.R:142:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L142) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) < 0L)
                                   ^~~
```
[R/plotMA-methods.R:157:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L157) *style:* **Variable or function name should be snake_case.**
```r
        log10BaseMean <- log10(data[["baseMean"]])
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:160:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L160) *style:* **Variable or function name should be snake_case.**
```r
        xBreaks <- 10L ^ seq(from = floor, to = ceiling, by = 1L)
        ^~~~~~~
```
[R/plotMA-methods.R:240:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L240) *style:* **Variable or function name should be snake_case.**
```r
            labelData <- data %>%
            ^~~~~~~~~
```
[R/plotMA-methods.R:275:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L275) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/plotMA-methods.R:315:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L315) *style:* **Variable or function name should be snake_case.**
```r
plotMeanAverage <- function(...) {
^~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:317:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L317) *warning:* **no visible global function definition for ‘plotMA’, Did you mean 'plot'?**
```r
    plotMA(...)
    ^~~~~~
```
[R/plotVolcano-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L78) *style:* **Variable or function name should be snake_case.**
```r
        pointColor = "gray50",
        ^~~~~~~~~~
```
[R/plotVolcano-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        sigPointColor = c(upregulated = "purple", downregulated = "orange"),
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:84:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L84) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotVolcano-methods.R:85:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L85) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:86:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L86) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotVolcano-methods.R:86:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L86) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotVolcano-methods.R:87:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L87) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:88:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L88) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(ylim)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:94:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L94) *warning:* **no visible global function definition for ‘assertIsImplicitInteger’**
```r
        assertIsImplicitInteger(ntop)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:95:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L95) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(c(lfcThreshold, ntop))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:97:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L97) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(pointColor)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:98:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L98) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(sigPointColor)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:100:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L100) *style:* **Variable or function name should be snake_case.**
```r
            sigPointColor <- c(
            ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:105:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L105) *warning:* **no visible global function definition for ‘assert_is_of_length’**
```r
        assert_is_of_length(sigPointColor, n = 2L)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:106:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L106) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(histograms)
        ^~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:111:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L111) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "svalue"  # nocov
            ^~~~~~~
```
[R/plotVolcano-methods.R:113:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L113) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "padj"
            ^~~~~~~
```
[R/plotVolcano-methods.R:117:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L117) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/plotVolcano-methods.R:118:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L118) *style:* **Variable or function name should be snake_case.**
```r
        negLogTestCol <- camel(paste("neg", "log10", testCol))
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:118:26:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L118) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**
```r
        negLogTestCol <- camel(paste("neg", "log10", testCol))
                         ^~~~~
```
[R/plotVolcano-methods.R:147:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L147) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) > 0L)
                                   ^~~
```
[R/plotVolcano-methods.R:149:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L149) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) < 0L)
                                   ^~~
```
[R/plotVolcano-methods.R:158:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L158) *style:* **Variable or function name should be snake_case.**
```r
        lfcHist <- ggplot(
        ^~~~~~~
```
[R/plotVolcano-methods.R:183:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L183) *style:* **Variable or function name should be snake_case.**
```r
        pvalueHist <- ggplot(
        ^~~~~~~~~~
```
[R/plotVolcano-methods.R:277:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L277) *style:* **Variable or function name should be snake_case.**
```r
            labelData <- data %>%
            ^~~~~~~~~
```
[R/plotVolcano-methods.R:331:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L331) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/show-methods.R:19:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L19) *style:* **Variable or function name should be snake_case.**
```r
.showHeader <- function(object, version = NULL) {
^~~~~~~~~~~
```
[R/show-methods.R:34:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L34) *style:* **Variable or function name should be snake_case.**
```r
        contrastNames <- .contrastNames(object)
        ^~~~~~~~~~~~~
```
[R/show-methods.R:34:26:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L34) *warning:* **no visible global function definition for ‘.contrastNames’, Did you mean 'contrastNames'?**
```r
        contrastNames <- .contrastNames(object)
                         ^~~~~~~~~~~~~~
```
[R/show-methods.R:58:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L58) *warning:* **local variable ‘deg’ assigned but may not be used**
```r
        deg <- slot(object, "deg")
        ^~~
```
[R/show-methods.R:66:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L66) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(results)
                    ^~~~~~~~~~~~
```
[R/show-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L68) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(results)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/show-methods.R:85:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L85) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
            assert_is_a_string(dirname)
            ^~~~~~~~~~~~~~~~~~
```
[R/show-methods.R:89:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L89) *warning:* **no visible global function definition for ‘showSlotInfo’**
```r
        showSlotInfo(list)
        ^~~~~~~~~~~~
```
[R/topTables-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L47) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResultsTables"))
        ^~~~~~~~~~~
```
[R/topTables-methods.R:50:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L50) *warning:* **no visible global function definition for ‘assertIsImplicitInteger’**
```r
        assertIsImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:53:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L53) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(results, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L68) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(keep, colnames(data))
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L69) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(deg, rownames(data))
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- slot(object, "rowRanges")
        ^~~~~~~~~
```
[R/topTables-methods.R:76:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L76) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- as(rowRanges, "DataFrame")
            ^~~~~~~
```
[R/topTables-methods.R:83:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L83) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset(rownames(data), rownames(rowData))
            ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:84:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L84) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- rowData[rownames(data), keep, drop = FALSE]
            ^~~~~~~
```
[R/topTables-methods.R:126:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L126) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:127:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L127) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(object)
                    ^~~~~~~~~~~~
```
[R/topTables-methods.R:128:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L128) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(contrast)
        ^~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:131:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L131) *warning:* **no visible global function definition for ‘.topTable’**
```r
        up <- .topTable(object, direction = "up", n = n)
              ^~~~~~~~~
```


Successfully aliased the URL <https://portal-nextjs-now-6rjnyzw62.now.sh> to the following alias.

* https://stagepage.now.sh


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wtf is this fucking entropy=? suck dix nature!


I think that `len` stand for length an therefore should be signed. Unsigned arithmetic exist to handle bitstream, not to represent non-negative number. If you need 32 bit to store this length, `int_fast64_t` is probably the best choice.


If `len` effectively stands for `lenght`, consider comparing it with numbers in base 10 (and put their value behind a constant).


This broke the buildbots: https://downloads.openwrt.org/snapshots/faillogs/mipsel_24kc/packages/libsndfile/compile.txt


this image is dead


Consider using `static_cast<uint8_t>` instead of C-style cast.


Consider using `using vec8 = std::vector<uint8_t>;`


Consider using `out.push_back()`.


CNAME file is added.


No need to prefix `stat` by `struct` since you are in a C++ header (you already used `namespace`), and thus don't need to be compatible with C syntax.


You should have your `vec8` alias visible globally and use it here too.


In every turn, each move has to be calculated anyway. It should be done once in the ChessBoard class and further be used as a cache.


Looks like our ships are able to be moved now, good job


Interestingly enough, ZFS (8.x) now has also added sysfs access to properties (uh), and the changes are not compatible with CONSTIFY. ex. struct sysfs_ops is always doconst. Not sure how they would fix that trivially but I found this while searching around. Also, something like pax_open/close should not be needed if the objects are allocated via kmalloc, AFAIK.


Interesting.  Seems like this will let us set stuff directly from the command line, so looks good to me. :smile:


I am nearly sure that this is undefined behavior, and you should use `memcpy` instead.


bool ?


Not sure why it shows a whole paragraph changed in diff, but I changed "statment" -> "statement", "asynchonous" -> "asynchronous"


Updating the typo


[R/export-methods.R:27:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/R/export-methods.R#L27) *style:* **Variable or function name should be lowerCamelCase.**
```r
export.DESeqAnalysis <- function(
^~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:32:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L32) *style:* **Commented code should be removed.**
```r
#             dir = "resultsTables"
              ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:34:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L34) *style:* **Commented code should be removed.**
```r
#         type = "output"
          ^~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:37:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L37) *style:* **Commented code should be removed.**
```r
#         head(28L)
          ^~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:119:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L119) *style:* **Commented code should be removed.**
```r
#             rdsToken = "token.rds"
              ^~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:121:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L121) *style:* **Commented code should be removed.**
```r
#         expect_true("dropboxFiles" %in% names(resTbl))
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:126:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L126) *style:* **Commented code should be removed.**
```r
#                 grepl("^https://www.dropbox.com/s/", file[["url"]])
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:128:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L128) *style:* **Commented code should be removed.**
```r
#             FUN.VALUE = logical(1L)
              ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:131:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L131) *style:* **Commented code should be removed.**
```r
#         output <- capture.output(.markdownResultsTables(resTbl))
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


It looks like you are reading `size` element of type `T`. I think the variable `size` should be named `numberofItem` or something in those lines.


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I think you can directly use `buf.buffer()` instead of `&buf.buffer()[0]` but I may be wrong here.


Successfully aliased the URL <https://podlove-web-player-ssnijxcwtx.now.sh> to the following alias.

* https://podlove-web-player.now.sh


You should consider moving your external dependencies in an `external` folder, to make it clear that it's not your business code (and that it can have a different license).


And news on Android support?


hola!
when I used the codes in my PC, why do they out the same results -8589993460???


You should extract the following code in a function (or more probably a lambda with reference capture since it's easier) to not have to duplicate it with the content of the above loop.


Необходимо было реализовать чат


Лучше сделать `attr_reader :type` в классе поезда. Тогда при вызове будет просто `train.type` вместо `train.type_of_train`


You sent the money. Can the sender circle around collect it again? I think so, because you haven't done the accounting. There is still money in the Box. If I were a bad guy, I would send a little money, then set up a robot to cancel, cancel, cancel until the contract is completely drained of funds. Yikes!


Заменить на `attr_reader :type`


[R/AllClasses.R:95:9:](https://github.com/hbc/bcbioSingleCell/blob/1267cb1378cec2299a26c529abd738b0c6fe74d4/R/AllClasses.R#L95) *style:* **TODO comments should be removed.**
```r
        # FIXME Ensure `sampleData` is moved to `colData`.
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/AllClasses.R:98:9:](https://github.com/hbc/bcbioSingleCell/blob/1267cb1378cec2299a26c529abd738b0c6fe74d4/R/AllClasses.R#L98) *style:* **TODO comments should be removed.**
```r
        # FIXME Switch to using basejump `checkSlotInfo()`.
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bcbioSingleCell.R:169:5:](https://github.com/hbc/bcbioSingleCell/blob/1267cb1378cec2299a26c529abd738b0c6fe74d4/R/bcbioSingleCell.R#L169) *style:* **TODO comments should be removed.**
```r
    # FIXME Add support for loading bcbio GTF (see bcbioRNASeq).
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/globals.R:16:3:](https://github.com/hbc/bcbioSingleCell/blob/1267cb1378cec2299a26c529abd738b0c6fe74d4/R/globals.R#L16) *style:* **Commented code should be removed.**
```r
# c("violin", "ridgeline", "ecdf", "histogram", "boxplot")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotBarcodeRanks-methods.R:20:1:](https://github.com/hbc/bcbioSingleCell/blob/1267cb1378cec2299a26c529abd738b0c6fe74d4/R/plotBarcodeRanks-methods.R#L20) *style:* **Variable or function name should be lowerCamelCase.**
```r
plotBarcodeRanks.SingleCellExperiment <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/show-methods.R:25:1:](https://github.com/hbc/bcbioSingleCell/blob/1267cb1378cec2299a26c529abd738b0c6fe74d4/R/show-methods.R#L25) *style:* **Variable or function name should be lowerCamelCase.**
```r
show.bcbioSingleCell <- function(object) {
^~~~~~~~~~~~~~~~~~~~
```


You can use a constexpr function instead of a macro here.


[R/autopadZeros-methods.R:30:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/autopadZeros-methods.R#L30) *style:* **Variable or function name should be lowerCamelCase.**
```r
autopadZeros.character <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~
```
[R/autopadZeros-methods.R:63:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/autopadZeros-methods.R#L63) *style:* **Variable or function name should be lowerCamelCase.**
```r
autopadZeros.matrix <- function(
^~~~~~~~~~~~~~~~~~~
```
[R/autopadZeros-methods.R:100:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/autopadZeros-methods.R#L100) *style:* **Variable or function name should be lowerCamelCase.**
```r
autopadZeros.SummarizedExperiment <- function(object, rownames = FALSE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/humanize-methods.R:30:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/humanize-methods.R#L30) *style:* **Variable or function name should be lowerCamelCase.**
```r
humanize.SummarizedExperiment <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeSampleData.R:40:7:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/makeSampleData.R#L40) *style:* **Commented code should be removed.**
```r
    # blacklist = c("interestingGroups", "sampleID")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


A general plan for each function.

1. Check everything is acceptable and allowed.
2. Address ALL of the effects ... update records, emit an event.
3. Transfer funds (if needed).
4. Return a response (e.g. `return true;`)


dead branch


Dead branch


При вызове `current_station` мы вызываем метод, который возвращает станцию. Индекс у нас хранит инстанс переменная `@current_station`. Лучше сделать так:
```
current_station.send_train(self)
@current_station += 1
current_station.receive_train(self)
```


В задании не сказано о том что необходимо считать именно инстансы конкретного класса а не любые поезда в целом, поэтому реализация сделана на максимальный охват аудитории.


Shouldn't it be  "nr_run_hysteresis = NR_RUN_HYSTERESIS_HEXA"  ???


I would like to show you a better way to do this before we move on. Let's tidy up the rest and then introduce some techniques you will want for the next project.


This function is way to long. Consider creating sub-function, split each section where you have a comment, and replace the comments by the name of the extracted function.


WTFPL


`return unless previous_station`


```
current_station.send_train(self)
@current_station -= 1
current_station.receive_train(self)
```


Consider removing dead code in comment.


it's not showing


saw approval from MonsieurNicolas
at https://github.com/MonsieurNicolas/stellar-core/commit/31d7c376b6e6f2ba2176d7f9453a5e3d43ffd3fa


merging MonsieurNicolas/stellar-core/newCheckers = 31d7c376 into auto


MonsieurNicolas/stellar-core/newCheckers = 31d7c376 merged ok, testing candidate = 4f9b7e51


Лишний `end`


It is the present below that swap front and back buffer. So I don't understand this comment


Проверка не нужна. При выходе за верхнюю границу массив и так вернет `nil`. Убрать строчку


Пробел перед закрывающей фигурной скобкой:
`@trains.count { |train| train.type_of_train == type }`


These logs should include everything someone/something would need to reconstruct the history of the contract state. Usually this follow a pattern.

1. One log for each function with names that clearly match up what goes with what.
2. All the inputs to the functions are important, so they should go in the log.
3. Usually `msg.sender` is important and sometimes `msg.value`.

This event doesn't show many of the inputs that created the box, so it would be possible to reconstruct the crime scene (think CSI) using only the logs.


MonsieurNicolas/stellar-core/newCheckers = 31d7c376 merged ok, testing candidate = 4e047dae


#5 Done


I think this should be `-50` because to you took 50 for the contract owner.


Maybe using unique_ptr would be nicer


Consider removing dead code. It is not tested, and thus may become out-of-sync with the rest of your code. Don't worry, git will remember it, and you can even tag the deletion commit for a quick search in your history.


[R/autopadZeros-methods.R:30:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/autopadZeros-methods.R#L30) *style:* **Variable or function name should be lowerCamelCase.**
```r
autopadZeros.character <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~
```
[R/autopadZeros-methods.R:63:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/autopadZeros-methods.R#L63) *style:* **Variable or function name should be lowerCamelCase.**
```r
autopadZeros.matrix <- function(
^~~~~~~~~~~~~~~~~~~
```
[R/autopadZeros-methods.R:100:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/autopadZeros-methods.R#L100) *style:* **Variable or function name should be lowerCamelCase.**
```r
autopadZeros.SummarizedExperiment <- function(object, rownames = FALSE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/humanize-methods.R:30:1:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/humanize-methods.R#L30) *style:* **Variable or function name should be lowerCamelCase.**
```r
humanize.SummarizedExperiment <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeSampleData.R:40:7:](https://github.com/steinbaugh/basejump/blob/48b5481a2c74fad334fa83c4a7f1a88f24743e26/R/makeSampleData.R#L40) *style:* **Commented code should be removed.**
```r
    # blacklist = c("interestingGroups", "sampleID")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


If renderosd is called once by frame there is no gain to force this cast.


[R/export-methods.R:27:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/R/export-methods.R#L27) *style:* **Variable or function name should be lowerCamelCase.**
```r
export.DESeqAnalysis <- function(
^~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:32:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L32) *style:* **Commented code should be removed.**
```r
#             dir = "resultsTables"
              ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:34:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L34) *style:* **Commented code should be removed.**
```r
#         type = "output"
          ^~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:37:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L37) *style:* **Commented code should be removed.**
```r
#         head(28L)
          ^~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:119:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L119) *style:* **Commented code should be removed.**
```r
#             rdsToken = "token.rds"
              ^~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:121:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L121) *style:* **Commented code should be removed.**
```r
#         expect_true("dropboxFiles" %in% names(resTbl))
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:126:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L126) *style:* **Commented code should be removed.**
```r
#                 grepl("^https://www.dropbox.com/s/", file[["url"]])
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:128:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L128) *style:* **Commented code should be removed.**
```r
#             FUN.VALUE = logical(1L)
              ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:131:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/15d608b0ca8446daa781f06d5cead474e3bd5000/tests/testthat/test_DESeqResultsTables.R#L131) *style:* **Commented code should be removed.**
```r
#         output <- capture.output(.markdownResultsTables(resTbl))
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


I was hoping you could test it also and see if it is not breaking anything. When you have time of course. :smiley:


merge_dict.py  -- merges the list of dictionaries obtained for each xml files of the articles
parse_articles.py -- parses the xml files for an article and outputs the factoids found and list of dictionaries containing information for each revision.
parse_articles_India.py -- parses the History section of xml files of India aticle
parse_hits_NGD -- parses the scraped ouput and calculated NGD values


В классе маршрута во второй строке вместо `station` должно быть  `stations`:
`attr_reader :stations`


Contains the LSA value of a subset of an article (50 factoids and their possible pairs)


Update test.js for correctly identified Android devices


stuff to do


Now could not deploy this pull request since the `now.json` file is empty.
It should be a valid JSON file.

    For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


@lionel-  do you still remember why you added this `add-file-local-variable`? Didn't you mean to make it permanent-local instead?


ok


Just like the picture
![wofha-181202-021840](https://user-images.githubusercontent.com/24326506/49331996-ae446f00-f5e0-11e8-91c8-66adfab93a4d.png)


Лишние отступы. Должно быть на одном уровне с `return`:
```
return if next_station.nil?
current_station.remove_train(self)
next_station.add_train(self)
@location += 1
```


Аналогично в методе движения вперед


FWIW, the value 0x00000280 was probably the block header size in bits (80*8). If so, should it really stay the same for Sapling's larger block headers? If things are working fine with Sapling despite this value staying the same, was/is it possibly unused?


[`openssl` 명령](create-security-certificates-openssl.html)을 사용하여 보안 인증서를 생성할 수 있습니다.

이렇게 바꾸는게 더 맞을 거 같습니다


@FittyFrank Great that my changes are useful for you. Have you committed your changes regarding the plus/minus icons? I can't seem to find your changes in your branch. I would like to introduce a third kind of icon. It should appear when the item itself is not selected, but some descendants are selected. Like in this example: http://objectlistview.sourceforge.net/cs/_images/hierarchical-checkboxes-1.png
I guess it may be useful to use your change as a basis for this.


You are cheater!!!
It is forbidden to push clean code before my review.
.
.
,


[CodeFactor](https://www.codefactor.io/repository/github/sanjeev1779/notification-website) found an issue: Space indentation expected

It's currently on:
[src\app\app-routing.module.ts:8
](https://www.codefactor.io/repository/github/sanjeev1779/notification-website/source/master/src/app/app-routing.module.ts#L8)Commit b542a75b35fbd0f31530afdcf0ca1867b02eb04d


Gross. Thanks Don!

On Saturday, December 1, 2018, Don Juan Javier <notifications@github.com>
wrote:

> @chiedo <https://github.com/chiedo> This seems to confirm my findings:
>
> https://shinglyu.github.io/web/2018/03/25/merge-pull-
> requests-without-merge-commits.html
>
> Under the hood, GitHub and GitLab’s “merge” button uses the --no-ff
> option, which will force create a merge commit.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/chiedolabs/eslint-config-node/commit/c1e3de7fca85bc5ce2336ec36a5d9e24746ee31c#commitcomment-31523789>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ACDokK3S2NRLf37IsciDOnNI6yt_PYPJks5u0rRogaJpZM4Y8Sbi>
> .
>

--
- Sent via mobile


Answering my own question: this value was first introduced in ee7b535ea62a569d97bb550c2e35a2c2ecb21f0b "Add Stratum support" and this commit includes introduction and use of a function `sha256d`, which apparently assumes pre-applied SHA-256 padding (where this value would indeed be the input size in bits). This is confirmed in pooler's answer in https://github.com/pooler/cpuminer/issues/82. So this value/field is probably unused for PoW schemes other than Bitcoin's double-SHA-256. Ditto about the many zeroes and 0x80000000. It's unclean to be doing this padding for other PoW schemes and with the wrong bit size, but it shouldn't hurt.


Successfully aliased the URL <https://wip-waqsfqbizn.now.sh> to the following alias.

* https://wip.now.sh


The /login path creates a token. Once the token is generated once the token is pasted within the authorization header as a bearer, a get request to /profile will be verified.


Congrats! If this does in fact scale well, can anyone explain *why* it scales well? I'm trying to understand better what properties make patches scale well.


شو هالتخبيص يا فهمان؟


Argument parsing is always a pain. Given that you manually wrote the help, you should take a look at th c++ port of [docopt](https://github.com/docopt/docopt.cpp). And if you want to generate manual page, take a look at [help2man](https://www.gnu.org/software/help2man/).


[R/AllClasses.R:105:29:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/AllClasses.R#L105) *style:* **TODO comments should be removed.**
```r
    contains = "DataFrame"  # FIXME SplitDataFrameList
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CellMarkers.R:67:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/CellMarkers.R#L67) *style:* **Variable or function name should be lowerCamelCase.**
```r
CellCycleMarkers <- function(object, gene2symbol) {
^~~~~~~~~~~~~~~~
```
[R/CellMarkers.R:82:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/CellMarkers.R#L82) *style:* **Variable or function name should be lowerCamelCase.**
```r
CellTypeMarkers <- function(object, gene2symbol) {
^~~~~~~~~~~~~~~
```
[R/cellTypesPerCluster-methods.R:24:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/cellTypesPerCluster-methods.R#L24) *style:* **Variable or function name should be lowerCamelCase.**
```r
cellTypesPerCluster.KnownMarkers <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffExp-methods.R:308:5:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/diffExp-methods.R#L308) *style:* **TODO comments should be removed.**
```r
    # TODO Switch to using `design()` generic.
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffExp-methods.R:334:5:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/diffExp-methods.R#L334) *style:* **TODO comments should be removed.**
```r
    # TODO Switch to using `design()` generic.
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/globals.R:21:3:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/globals.R#L21) *style:* **Commented code should be removed.**
```r
# viridis::scale_colour_viridis(direction = -1L)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotFeature-methods.R:29:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotFeature-methods.R#L29) *style:* **Variable or function name should be lowerCamelCase.**
```r
.plotFeature.SingleCellExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotFeature-methods.R:93:5:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotFeature-methods.R#L93) *style:* **TODO comments should be removed.**
```r
    # FIXME Need to add pointsAsNumbers support.
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:57:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotGene-methods.R#L57) *style:* **Variable or function name should be lowerCamelCase.**
```r
plotGene.SingleCellExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:102:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotGene-methods.R#L102) *style:* **Variable or function name should be lowerCamelCase.**
```r
plotDot.SingleCellExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:207:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotGene-methods.R#L207) *style:* **Variable or function name should be lowerCamelCase.**
```r
plotViolin.SingleCellExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:329:11:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotGene-methods.R#L329) *style:* **Put spaces around all infix operators.**
```r
        f ="plotGene",
          ^~
```
[R/plotMarker-methods.R:41:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotMarker-methods.R#L41) *style:* **Variable or function name should be lowerCamelCase.**
```r
plotMarker.SingleCellExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotMarker-methods.R:65:5:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotMarker-methods.R#L65) *style:* **TODO comments should be removed.**
```r
    # FIXME This step is breaking.
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotReducedDim-methods.R:62:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotReducedDim-methods.R#L62) *style:* **Variable or function name should be lowerCamelCase.**
```r
.plotReducedDim.SingleCellExperiment <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotReducedDim-methods.R:217:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotReducedDim-methods.R#L217) *style:* **Variable or function name should be lowerCamelCase.**
```r
.plotPCA.SingleCellExperiment <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotReducedDim-methods.R:228:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotReducedDim-methods.R#L228) *style:* **Variable or function name should be lowerCamelCase.**
```r
.plotTSNE.SingleCellExperiment <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotReducedDim-methods.R:237:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/plotReducedDim-methods.R#L237) *style:* **Variable or function name should be lowerCamelCase.**
```r
.plotUMAP.SingleCellExperiment <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/runZinbwave-methods.R:168:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/runZinbwave-methods.R#L168) *style:* **Variable or function name should be lowerCamelCase.**
```r
runZinbwave.seurat <- function(Y, ...) {
^~~~~~~~~~~~~~~~~~
```
[R/runZinbwave-methods.R:168:32:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/runZinbwave-methods.R#L168) *style:* **Variable or function name should be lowerCamelCase.**
```r
runZinbwave.seurat <- function(Y, ...) {
                               ^
```
[R/SeuratMarkers.R:47:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/SeuratMarkers.R#L47) *style:* **Variable or function name should be lowerCamelCase.**
```r
SeuratMarkers <- function(
^~~~~~~~~~~~~
```
[R/SeuratMarkers.R:172:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/R/SeuratMarkers.R#L172) *style:* **Variable or function name should be lowerCamelCase.**
```r
SeuratMarkersPerCluster <- SeuratMarkers
^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_cluster_statistics.R:4:3:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/tests/testthat/test_cluster_statistics.R#L4) *style:* **Commented code should be removed.**
```r
# data(sce, package = "basejump.data", envir = environment())
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_cluster_statistics.R:9:1:](https://github.com/steinbaugh/pointillism/blob/bbacf721a6d25d4d6ff052e814bcc7717b722669/tests/testthat/test_cluster_statistics.R#L9) *style:* **Variable or function name should be lowerCamelCase.**
```r
group_vars <- dplyr::group_vars
^~~~~~~~~~
```


معلللم


Quand tu as un retour booléen lié à une condition, n'hésite pas à simplifier :

``` js
return y < 500 && y >= 0 && x >= 0 && x < 650;
```

J'en profite également pour enlever toutes les parenthèses superflues, en m'appuyant sur les [règles de précédence](https://developer.mozilla.org/fr/docs/Web/JavaScript/Reference/Op%C3%A9rateurs/Pr%C3%A9c%C3%A9dence_des_op%C3%A9rateurs).


Tess


added Digi-Key's section for hardware


C'est un détail, mais je t'invite à ajouter un espace après les `:` dans les objets, pour faciliter la lecture.


You should re-open a raw string literal to be consistent.


Attention à l'indentation (toujours dans un soucis de faciliter la lecture du code) :

``` js
switch (condition) {
  case valeur:
    // instructions
    // du case
    // indentées
    break;
  case valeur2:
    // …
    break;
}


Pareil ici :

``` js
if (game.isInside(nextBloc[0], nextBloc[1])) {
  // …
}
```

est un peu plus facile à lire que "estunpeuplusfacileàlire" ;)


There were the following issues with your Pull Request

  * A "License" and a "Signed-off-by" trailers are required. See [the guidelines about this](https://github.com/ipfs/community/blob/master/contribution-guidelines.md#a-license-and-a-signed-off-by-trailers-are-required)

We ask for a few features in the commit message for Open Source licensing hygiene and commit message clarity.
`git commit --amend` can often help you quickly improve the commit message.
[Guidelines](https://github.com/ipfs/community/blob/master/contribution-guidelines.md#commit-messages) and [a script](https://github.com/ipfs/community/blob/master/dev/hooks/setup_commit_msg_hook.sh) are available to help in the long run.
Your feedback on GitCop is welcome on [this issue](https://github.com/ipfs/infrastructure/issues/23).

---
This message was auto-generated by https://gitcop.com


Bien joué !


I only reverted this commit as it was not properly done.  The source changes will still be appended in the coming commits, however.


from home


This breaks the build - see issue #528 .  Really should have been filed as a pull request so that build checks could have been done against the changes.


Si la clé d'un objet ne contient pas d'espace ou de caractères exotiques, tu peux te passer des guillemets.

``` js
var model = {
  beginner: [ … ],
  advanced: [ … ]
};
```


Valable pour JavaScript bien sûr, ce n'est pas le cas en PHP ^^


Pas besoin de passer `game.level` en paramètre, vu que cette information est accessible partout dans l'objet :) Donc les quatre fonctions de déplacement peuvent directement y accéder.


TeamCity ImageHunt / Build [Build 100](http://51.255.204.38:8111/viewLog.html?buildId=356&buildTypeId=ImageHunt_BuildPullRequest) is now running


![](https://github.trello.services/images/mini-trello-icon.png) [User should see main menu.](https://trello.com/c/I2DIDFR3/6-user-should-see-main-menu)


https://www.youtube.com/watch?v=HSZ9W8v7y9I :p


What are reason for removing text about Go language?


@SvitEM А зачем так много? ))


Bien joué :+1:


![](https://github.trello.services/images/mini-trello-icon.png) [User should be able to create a new game.](https://trello.com/c/eytZBKdC/9-user-should-be-able-to-create-a-new-game)


TeamCity ImageHunt / Build [Build 100](http://51.255.204.38:8111/viewLog.html?buildId=356&buildTypeId=ImageHunt_BuildPullRequest) outcome was **SUCCESS**
Summary: Tests passed: 413, ignored: 1 Build time: 00:02:58


@Mapach3 buenísimo.


Bit more than minor changes here - included some hoops/dropshot specific code to prevent field sizes being hardcoded to soccar


In this case hex is preferable since it more clearly shows when bits are not enough


## Joker
Este es mi villano favorito


Android app that showcases About MLH


can't store data from input values in state :/


Ok thanks!