[R/AllClasses.R:1:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:76:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:166:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:173:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/alphaSummary-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqAnalysis.R#L49) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqAnalysis"))
    ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L69) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResults"))
        ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L70) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(c("log2FoldChange", "padj"), colnames(object))
        ^~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:71:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L71) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:72:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L72) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:73:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L73) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:74:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L74) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:75:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L75) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L78) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/DESeqResultsTables-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        testCol <- "padj"
        ^~~~~~~
```
[R/DESeqResultsTables-methods.R:80:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L80) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        lfc <- sym(lfcCol)
               ^~~
```
[R/DESeqResultsTables-methods.R:81:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L81) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        test <- sym(testCol)
                ^~~
```
[R/DESeqResultsTables-methods.R:130:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L130) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:159:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L159) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- rowRanges(data)
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:169:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L169) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
        mcols(rowRanges) <- mcols
        ^~~~~
```
[R/DESeqResultsTables-methods.R:170:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L170) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
        assert_is_non_empty(rowRanges)
        ^~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:187:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L187) *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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:54:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:82:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:111:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/topTables-methods.R#L131) *warning:* **no visible global function definition for ‘.topTable’**
```r
        up <- .topTable(object, direction = "up", n = n)
              ^~~~~~~~~
```


>we already have a comment regarding overriding order. Ok then, will do the first option.

"The first option" was about `args[arg] = val`, right?

> move the rules about "argument A overrides argument B" into another hash (again, preferably inside pyDKB, not here) and make a single function which makes tests for arguments' interaction basing on this hash.

Not sure that testing `pyDKB` basing on the `pyDKB` internals is a good idea. If I change this internal hash, test will still be passable even if my change breaks the logic that is described in help/usage message -- while it is exactly what it should check.
If the logic was changed, the one who did it must be notified (to avoid unintended changes).


merge assassino, mi piace


Sorry, that line is already gone. Working through the commit history, this sometimes happens. Apologies.


`System.Net.ServicePointManager.SecurityProtocol |= SecurityProtocolType.Tls12;`


first


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/623ac46c-aeaa-4433-a262-223430c2e0af?env_id=ibm%3Ayp%3Aus-south "googleDictionaryAPI"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/43a8bfc9-4989-4464-8299-979f59631a9c?env_id=ibm%3Ayp%3Aus-south "googleDictionaryAPI") deployed [googleDictionaryAPI](https://github.com/meetDeveloper/googleDictionaryAPI/releases/tag/deploy-ibm-yp-eu-gb-lifeplusplus-API-s-20181121-120602 "deploy-ibm-yp-eu-gb-lifeplusplus-API-s-20181121-120602") to [API's](https://console.bluemix.net/apps/0971aef0-04d8-454a-b263-f77d06d21309?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:lifeplusplus:API's"), including this commit


it is not the fact I didn't know, its the fact that you have only just added it in, to make it appear i "didn't know".
Feature is normally a visible change or addition that the client wanted or something that improve the user experience, a feature is something that is something new. What I did, was a Fix, not a hot fix nor a feature, but a Fix. A modification to the code to enable it to work correctly and as expected, not adding to the expectation of the users. thus not a feature.


Thanks for this! Just found this myself today 👍


@dmknght you are totally right. this is actually a bug and i can fix it. thank you so much for pointing this out and be patient until the fix comes :)