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[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)
              ^~~~~~~~~
```


jeśli masz sytuację, że chcesz obsłużyć brak wartości podając jakąś inną to lepiej użyć `.orElseGet` żeby Ci nie tworzyło bez potrzeby nowego obiektu


Aliasing failed with the following error:

~~~
Error! We couldn't verify the domain brunaldi.me.
~~~


`String.format("%s/members/%s/boards",trelloApiEndpoint,username)`


Thanks for the add @DanielMSchmidt  happy to help maintain!


исправлено


![](https://github.trello.services/images/mini-trello-icon.png) [Верстка страницы и привязка к API](https://trello.com/c/HWU1xmvm/11-%D0%B2%D0%B5%D1%80%D1%81%D1%82%D0%BA%D0%B0-%D1%81%D1%82%D1%80%D0%B0%D0%BD%D0%B8%D1%86%D1%8B-%D0%B8-%D0%BF%D1%80%D0%B8%D0%B2%D1%8F%D0%B7%D0%BA%D0%B0-%D0%BA-api)


jeśli chodzi o trzymanie tokenów dostępowych w githubie to jest to bardzo poważny antypattern ;) Jak skończysz kurs wygeneruj nowy apikey na trello na swoim koncie


IBM Cloud [toolchain](https://console.stage1.bluemix.net/devops/toolchains/c035403f-8201-4c5a-a95c-6236dd99760c?env_id=ibm%3Ays1%3Aus-south "stageNg-devInsightOrg-20181128"): [Delivery Pipeline](https://console.stage1.bluemix.net/devops/pipelines/757d1730-2b06-4946-bcfc-be17aeb534a0?env_id=ibm%3Ays1%3Aus-south "stageNg-devInsightOrg-20181128") deployed [stageNg-devInsightOrg-20181128](https://github.com/testid12345/stageNg-devInsightOrg-20181128/releases/tag/deploy-ibm-ys1-us-south-giang-us.ibm.com-stageNgPaid-20181128-184220 "deploy-ibm-ys1-us-south-giang-us.ibm.com-stageNgPaid-20181128-184220") to [stageNgPaid](https://console.stage1.ng.bluemix.net/apps/6226888e-95e0-4271-859f-1d8d6b097c6c?env_id=ibm:ys1:us-south "ibm:ys1:us-south:giang@us.ibm.com:stageNgPaid"), including this commit


Error Handling*


Clarification: the connection I am referring to for URL configuration is originally seen in 02dabec.

For Django 2.1, the inclusion path would become:

```python
path("blog/", include(blog_urls)),
```


Hello my name is Lena


as an approver you can see the email address of people submitting patches (click on their username). You can similarly block users.

BTW, in this context you can, once logged in, also click on the 'pending' link, and unblock users. Initially they are all blocked, and must be unblocked (which we kind of do by default, since we have no other info).


downlo


what about first testing this with 8 threads? Very few workers have 15 threads.


NICE MOVES


Maybe to use $task instead of $tasks (see iterator some lines above)


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

* https://distseq.now.sh


Awesome. Thx. I sent him\her an email and will try to help.

On Wed, Nov 28, 2018, 11:44 AM Joost VandeVondele <notifications@github.com
wrote:

> as an approver you can see the email address of people submitting patches
> (click on their username). You can similarly block users.
>
> BTW, in this context you can, once logged in, also click on the 'pending'
> link, and unblock users. Initially they are all blocked, and must be
> unblocked (which we kind of do by default, since we have no other info).
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/protonspring/Stockfish/commit/f4fff8f7bd64d9dea1584cccfebd4d0d3f12a144#commitcomment-31488542>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AcVnSA9htEtRPacYJUBqXpClADwcYSEbks5uztmYgaJpZM4Y30k9>
> .
>


Some covers have large size. Option "cover size" should solve this problem.
8 mb https://f4.bcbits.com/img/a0523520394_0.jpg
5.9 mb https://is3-ssl.mzstatic.com/image/thumb/Music128/v4/52/76/d9/5276d9af-383f-ed42-d708-38129ef585a7/source/100000x100000-999.jpg
5 mb https://is3-ssl.mzstatic.com/image/thumb/Music118/v4/5a/c5/3f/5ac53f2f-02b0-4729-e9ce-83994da4ec5b/source/100000x100000-999.jpg
11 mb https://is1-ssl.mzstatic.com/image/thumb/Music128/v4/4b/ff/25/4bff25a1-127a-0784-5b29-bdfd95dfc7b2/source/100000x100000-999.jpg
9 mb https://f4.bcbits.com/img/a0245417581_0.jpg
8.5 mb https://f4.bcbits.com/img/a3559459035_0


I saw that default is stm, not sure if it's correct. But you're right, not in the scope of this patch.


@samtstern Can we use string templating here?
I'll be happy to send a quick fix


I thought about that.  8 threads would test this a little, but 15 would be
much better.  I'm in no hurry at all, so I thought it would be OK.

Should I cancel it and submit for 8 threads?

On Wed, Nov 28, 2018 at 11:45 AM Joost VandeVondele <
notifications@github.com> wrote:

> what about first testing this with 8 threads? Very few workers have 15
> threads.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/protonspring/Stockfish/commit/865770436aa75657fa97333e4cabd84e3ae8e572#commitcomment-31488555>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AcVnSGqaRHQxNsekigbFO8XujsNZa277ks5uztnIgaJpZM4Y4Nz->
> .
>

--
Michael T. Whiteley
mobile: 801.707.6886


Can be replaced with a single line function as;
```
override fun onChildRemoved(dataSnapshot: DataSnapshot) = Unit
```
Same for methods below


@MladenPetronijevic these still say 'status hackathon' on them.  can you remove that text?


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


@mysticatea Thank you for addressing this! 🙌


That method is completely useless now, and keeping it for the sake of mod compatibility is pointless.  Dynamic Surroundings has already updated to use a newly added method anyway.  Also, no one is forcing you to update your mods immediately, and if a mod becomes incompatible for a short time, just downgrade.  It's not the end of the world.


*Update*: Doing this patch:
```diff
--- a/src/input/virtual_input.h 2018-11-28 16:14:12
+++ b/src/input/virtual_input.h 2018-11-28 18:49:23
@@ -59,7 +59,7 @@
             else
                 data_tmpSize = static_cast<size_t>(recordBuffer->GetRingBufferReadAvailable());

-            uint8_t data_tmp[data_tmpSize];
+            uint8_t data_tmp[1024*sizeof(float)];
             recordBuffer->getDataFromBuffer(data_tmp, data_tmpSize);
             rawStream.write((char *) data_tmp, data_tmpSize);
         }
```

fixed the stack-overflow.


here i can write a reason for the updates i made


ncmpcpp config


Successfully aliased the URL <https://material-theme-site-6kqlmoned.now.sh> to the following aliases.

* https://material-theme.site
* https://www.material-theme.site


ipdb


Does it show pacman? :D


👍 You should also be added to the team in this org, did that work properly?