[R/dEploidPlotly.R:26:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L26) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:28:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L28) *style:* **Variable or function name should be snake_case.**
```r
    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~
```
[R/dEploidPlotly.R:93:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L93) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:93:32:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L93) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~
```
[R/dEploidPlotly.R:95:3:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L95) *style:* **Variable or function name should be snake_case.**
```r
  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:97:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L97) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:97:27:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L97) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^
```
[R/dEploidPlotly.R:97:29:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L97) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^
```
[R/dEploidPlotly.R:159:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L159) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:159:40:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L159) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~
```
[R/dEploidPlotly.R:208:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:208:34:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~
```
[R/dEploidPlotly.R:208:43:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~
```
[R/DEploidR.R:23:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:23:36:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:23:49:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~
```
[R/DEploidR.R:54:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:54:36:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:54:49:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~
```
[R/DEploidR.R:62:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L62) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:66:13:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L66) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:83:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L83) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:84:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L84) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:86:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L86) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:87:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L87) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:114:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
^~~~~~~~~~~
```
[R/DEploidR.R:114:25:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L151) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:152:24:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~
```
[R/DEploidR.R:152:37:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~
```
[R/DEploidR.R:152:51:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~
```
[R/DEploidR.R:153:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L153) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:200:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L200) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:201:21:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:201:40:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:202:21:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:202:46:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~
```
[R/DEploidR.R:202:59:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~
```
[R/DEploidR.R:203:21:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L203) *style:* **Variable or function name should be snake_case.**
```r
                    cex.axis = 1){
                    ^~~~~~~~
```
[R/DEploidR.R:207:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L207) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:266:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:266:22:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~
```
[R/DEploidR.R:268:17:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~
```
[R/DEploidR.R:268:30:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~
```
[R/DEploidR.R:268:44:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~
```
[R/DEploidR.R:269:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L269) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:271:9:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L271) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:271:31:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^
```
[R/DEploidR.R:271:33:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^
```
[R/DEploidR.R:323:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:323:34:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~
```
[R/DEploidR.R:323:43:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~
```
[R/DEploidR.R:324:23:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L324) *style:* **Variable or function name should be snake_case.**
```r
                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:325:23:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:325:36:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:325:50:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:368:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L368) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:373:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:373:28:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~
```
[R/DEploidR.R:373:37:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~
```
[R/DEploidR.R:375:23:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:375:36:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:375:50:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:411:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L411) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~
```
[R/DEploidR.R:432:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:30:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:66:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~
```
[R/DEploidR.R:433:25:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L433) *style:* **Variable or function name should be snake_case.**
```r
                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:434:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:435:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~
```
[R/DEploidR.R:437:9:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L437) *style:* **Variable or function name should be snake_case.**
```r
        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~
```
[R/DEploidR.R:438:9:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L438) *style:* **Variable or function name should be snake_case.**
```r
        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~
```
[R/DEploidR.R:446:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L446) *style:* **Variable or function name should be snake_case.**
```r
    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~
```
[R/DEploidR.R:449:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/R/DEploidR.R#L449) *style:* **Variable or function name should be snake_case.**
```r
    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/liuyingh/DEploid-r/blob/b7c249c9c09497c39bc919a945f6f5e2f9ec17a7/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


Can we not pass CLI ctx into vxlan package?


pass a default value here.
vxlan.DefaultVNI


See here for example: https://github.com/leodotcloud/rancher-net/blob/ipsec_config_options/main.go#L88


See example: https://github.com/leodotcloud/rancher-net/blob/ipsec_config_options/main.go#L184


You missed answers[10]


The challenge/matchmaking functions should probably be screwed around to make it easier to pass teams around. `user.team` should probably straight-up not exist.

Maybe a `Challenge` class?


![](https://github.trello.services/images/mini-trello-icon.png) [Show bot invite in a!about](https://trello.com/c/mqzTOYFA/35-show-bot-invite-in-aabout)


See #1162


Can you describe what's wrong? Maybe I'll understand without a test case. I'll probably need a description even with a test case, anyway.


I deleted this for an important reason ;-) I think there may not be much point in having `auto-step` call that rule, because the user has to supply the motive; the problem is that when this subgoal appears to the user, it has come out of nowhere and the user doesn't have any context for understanding what kind of term they need to supply.

So I think it is better for `auto` not to call this rule, and for the user to call it manually. Later on, we can design the auto tactic to do some more fancy heuristics to figure out a motive... But for now, I'd rather just let the user intervene, and then resume `auto` after calling the rule by hand.


But if you feel differently, feel free to leave this.


@agentm Is it not possible to work with both 0.5 and 0.4?


[R/dEploidPlotly.R:26:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L26) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:28:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L28) *style:* **Variable or function name should be snake_case.**
```r
    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~
```
[R/dEploidPlotly.R:93:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L93) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:93:32:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L93) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~
```
[R/dEploidPlotly.R:95:3:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L95) *style:* **Variable or function name should be snake_case.**
```r
  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:97:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L97) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:97:27:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L97) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^
```
[R/dEploidPlotly.R:97:29:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L97) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^
```
[R/dEploidPlotly.R:159:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L159) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:159:40:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L159) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~
```
[R/dEploidPlotly.R:208:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:208:34:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~
```
[R/dEploidPlotly.R:208:43:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~
```
[R/DEploidR.R:23:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:23:36:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:23:49:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~
```
[R/DEploidR.R:54:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:54:36:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:54:49:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~
```
[R/DEploidR.R:62:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L62) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:66:13:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L66) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:83:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L83) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:84:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L84) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:86:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L86) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:87:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L87) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:114:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
^~~~~~~~~~~
```
[R/DEploidR.R:114:25:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L151) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:152:24:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~
```
[R/DEploidR.R:152:37:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~
```
[R/DEploidR.R:152:51:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~
```
[R/DEploidR.R:153:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L153) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:200:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L200) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:201:21:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:201:40:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:202:21:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:202:46:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~
```
[R/DEploidR.R:202:59:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~
```
[R/DEploidR.R:203:21:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L203) *style:* **Variable or function name should be snake_case.**
```r
                    cex.axis = 1){
                    ^~~~~~~~
```
[R/DEploidR.R:207:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L207) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:266:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:266:22:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~
```
[R/DEploidR.R:268:17:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~
```
[R/DEploidR.R:268:30:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~
```
[R/DEploidR.R:268:44:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~
```
[R/DEploidR.R:269:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L269) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:271:9:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L271) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:271:31:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^
```
[R/DEploidR.R:271:33:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^
```
[R/DEploidR.R:323:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:323:34:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~
```
[R/DEploidR.R:323:43:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~
```
[R/DEploidR.R:324:23:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L324) *style:* **Variable or function name should be snake_case.**
```r
                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:325:23:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:325:36:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:325:50:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:368:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L368) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:373:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:373:28:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~
```
[R/DEploidR.R:373:37:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~
```
[R/DEploidR.R:375:23:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:375:36:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:375:50:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:411:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L411) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~
```
[R/DEploidR.R:432:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:30:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:66:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~
```
[R/DEploidR.R:433:25:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L433) *style:* **Variable or function name should be snake_case.**
```r
                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:434:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:435:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~
```
[R/DEploidR.R:437:9:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L437) *style:* **Variable or function name should be snake_case.**
```r
        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~
```
[R/DEploidR.R:438:9:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L438) *style:* **Variable or function name should be snake_case.**
```r
        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~
```
[R/DEploidR.R:446:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L446) *style:* **Variable or function name should be snake_case.**
```r
    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~
```
[R/DEploidR.R:449:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/R/DEploidR.R#L449) *style:* **Variable or function name should be snake_case.**
```r
    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/243d5e3c6cd24ba1f10732a35050e98aec8eff2e/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


Fix can not generate the parser_cli to parse the modules/drivers/gnss/test_data/novatel.bin


넵.! 진행해보겠습니다.


I see. Should we remove other lines as well, such as `WIF` and `S1_REC`? The `Bool.ElimEq` in theory has the same problem but currently it only handles the non-dependent case.


See 2056bd423: ``user.team`` now is only read once per validation, in the command after ``/utm``.


Why don't Arceus formes auto-get items?

Oh, I remember now; they used to, but then Z crystals were introduced, so the item is now ambiguous.


Bluemix [toolchain](https://console-regional.ng.bluemix.net/devops/toolchains/de742651-8462-4286-b78d-3e94ac013f9f "compromisos"): [Delivery Pipeline](https://console-regional.ng.bluemix.net/devops/pipelines/0d0e8b6d-930b-40fc-ac1c-2a7d8ad5ef0b "compromisos") deployed [compromisos](https://github.com/eschuler7/compromisos/releases/tag/deploy-ibm-yp-us-south-eschuler-pe.ibm.com-dev-20170808-013613 "deploy-ibm-yp-us-south-eschuler-pe.ibm.com-dev-20170808-013613") to [dev](https://console.bluemix.net/apps/6f3a0e56-815a-41fc-aa5f-5ec09678068d?env_id=ibm:yp:us-south "ibm:yp:us-south:eschuler@pe.ibm.com:dev"), including this commit


Hello! in if (!PyArg_ParseTuple(args, "p: what is the "p"? I'm used to see i for int iirc


@favonia Good question; my suggestion is that as a rule of thumb (perhaps not universally perfect), any rule which produces subgoals which are not decomposed by the `auto-step` tactic should be removed. For instance, any rule which produces a `TERM` subgoal should not be called by `auto-step` for now.


Yes, it probably shouldn't be used at all, and in general, passing lots of arguments around is probably an antipattern. Some sort of `HalfBattle` class to represent a user and a team, that should be passed around by the matchmaker and challenge systems.


hey @JGilbert-eLife , I definitely prefer hyphens to underscores as well, but could you let dev know if the names of the reports output by this script change in future? lax relies on a certain naming pattern to find them and ingest them.

don't feel constrained in the types of changes you can make or worry if it breaks somebody's integration, just send us a link to the commits you've made and we'll fix anything up.


I didn't tested yet but it sounds great! Thanks!


[R/dEploidPlotly.R:26:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L26) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:28:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L28) *style:* **Variable or function name should be snake_case.**
```r
    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~
```
[R/dEploidPlotly.R:93:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L93) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:93:32:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L93) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~
```
[R/dEploidPlotly.R:95:3:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L95) *style:* **Variable or function name should be snake_case.**
```r
  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:97:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L97) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:97:27:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L97) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^
```
[R/dEploidPlotly.R:97:29:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L97) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^
```
[R/dEploidPlotly.R:159:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L159) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:159:40:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L159) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~
```
[R/dEploidPlotly.R:208:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:208:34:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~
```
[R/dEploidPlotly.R:208:43:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/dEploidPlotly.R#L208) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~
```
[R/DEploidR.R:23:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:23:36:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:23:49:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~
```
[R/DEploidR.R:54:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:54:36:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:54:49:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~
```
[R/DEploidR.R:62:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L62) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:66:13:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L66) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:83:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L83) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:84:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L84) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:86:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L86) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:87:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L87) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:114:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
^~~~~~~~~~~
```
[R/DEploidR.R:114:25:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L151) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:152:24:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~
```
[R/DEploidR.R:152:37:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~
```
[R/DEploidR.R:152:51:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~
```
[R/DEploidR.R:153:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L153) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:200:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L200) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:201:21:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:201:40:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:202:21:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:202:46:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~
```
[R/DEploidR.R:202:59:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~
```
[R/DEploidR.R:203:21:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L203) *style:* **Variable or function name should be snake_case.**
```r
                    cex.axis = 1){
                    ^~~~~~~~
```
[R/DEploidR.R:207:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L207) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:266:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:266:22:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~
```
[R/DEploidR.R:268:17:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~
```
[R/DEploidR.R:268:30:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~
```
[R/DEploidR.R:268:44:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~
```
[R/DEploidR.R:269:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L269) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:271:9:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L271) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:271:31:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^
```
[R/DEploidR.R:271:33:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^
```
[R/DEploidR.R:323:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:323:34:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~
```
[R/DEploidR.R:323:43:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~
```
[R/DEploidR.R:324:23:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L324) *style:* **Variable or function name should be snake_case.**
```r
                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:325:23:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:325:36:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:325:50:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:368:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L368) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:373:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:373:28:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~
```
[R/DEploidR.R:373:37:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~
```
[R/DEploidR.R:375:23:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:375:36:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:375:50:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:411:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L411) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~
```
[R/DEploidR.R:432:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:30:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:66:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~
```
[R/DEploidR.R:433:25:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L433) *style:* **Variable or function name should be snake_case.**
```r
                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:434:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:435:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~
```
[R/DEploidR.R:437:9:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L437) *style:* **Variable or function name should be snake_case.**
```r
        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~
```
[R/DEploidR.R:438:9:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L438) *style:* **Variable or function name should be snake_case.**
```r
        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~
```
[R/DEploidR.R:446:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L446) *style:* **Variable or function name should be snake_case.**
```r
    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~
```
[R/DEploidR.R:449:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/R/DEploidR.R#L449) *style:* **Variable or function name should be snake_case.**
```r
    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/699771700071045231f5b1d4860c36a23c1966d8/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


Hi Kevin, first of all thanks for the awesome tutorial, I'm learning a lot! I've run into a small problem here, is this an extra `ul` here? For some reason I can't get my anchor tags to work on `nav-footer`.


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