[R/dEploidPlotly.R:26:1:](https://github.com/liuyingh/DEploid-r/blob/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/liuyingh/DEploid-r/blob/9c56e630e5e050f5f40e2d78594f2adafd496519/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/liuyingh/DEploid-r/blob/9c56e630e5e050f5f40e2d78594f2adafd496519/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/liuyingh/DEploid-r/blob/9c56e630e5e050f5f40e2d78594f2adafd496519/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/9c56e630e5e050f5f40e2d78594f2adafd496519/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


- Some small style changes to modals/themes, I'm not exactly sure what it entails.
- Small changes to video calling.

### New strings
- A lot of empty strings in many languages are now filled.
- A ton of new member join system messages:
```js
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_21: "Challenger approaching - [!!{username}!!](usernameOnClick) has appeared!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_22: "It's a bird! It's a plane! Nevermind, it's just [!!{username}!!](usernameOnClick).",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_23: "It's [!!{username}!!](usernameOnClick)! Praise the sun! [T]/",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_24: "Never gonna give [!!{username}!!](usernameOnClick) up. Never gonna let [!!{username}!!](usernameOnClick) down.",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_25: "Ha! [!!{username}!!](usernameOnClick) has joined! You activated my trap card!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_26: "Cheers, love! [!!{username}!!](usernameOnClick)'s here!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_27: "Hey! Listen! [!!{username}!!](usernameOnClick) has joined!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_28: "We've been expecting you [!!{username}!!](usernameOnClick)",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_29: "It's dangerous to go alone, take [!!{username}!!](usernameOnClick)!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_30: "[!!{username}!!](usernameOnClick) has joined the server! It's super effective!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_31: "Cheers, love! [!!{username}!!](usernameOnClick) is here!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_32: "[!!{username}!!](usernameOnClick) is here, as the prophecy foretold.",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_33: "[!!{username}!!](usernameOnClick) has arrived. Party's over.",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_34: "Ready player [!!{username}!!](usernameOnClick)",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_35: "[!!{username}!!](usernameOnClick) is here to kick butt and chew bubblegum. And [!!{username}!!](usernameOnClick) is all out of gum.",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_36: "Hello. Is it [!!{username}!!](usernameOnClick) you're looking for?",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_37: "[!!{username}!!](usernameOnClick) has joined. Stay a while and listen!",
SYSTEM_MESSAGE_GUILD_MEMBER_JOIN_38: "Roses are red, violets are blue, [!!{username}!!](usernameOnClick) joined this server with you",
```


[R/dEploidPlotly.R:26:1:](https://github.com/liuyingh/DEploid-r/blob/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/liuyingh/DEploid-r/blob/6d6589dcda5cc04768d854e848fa903d7dc59493/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/liuyingh/DEploid-r/blob/6d6589dcda5cc04768d854e848fa903d7dc59493/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/liuyingh/DEploid-r/blob/6d6589dcda5cc04768d854e848fa903d7dc59493/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/6d6589dcda5cc04768d854e848fa903d7dc59493/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


Self note: change to continue;


Putting the test function at multiple places in AppBody.js doesn't work. It somehow affects the pano as well as the pano is not displayed after the test is run.


would you be against automating this?
eg. `$CurrentYear()`
```
public function CurrentYear() {
		return date('Y');
	}
```


https://www.youtube.com/watch?v=z8RkR4rd7dM

#MakeUlduarGreatAgain


In the license?


Per comments on #346, I've pulled all the global variables into `comms_globals.h`.  This will eventually form part of a `pm3_connection` struct (but probably more aptly named, a `pm3_context`), as part of the next stage.

But for now, these are still all global variables as the target of this PR has been:

1. Refactor all the communication logic, and.
2. To move all of the globals into a single file before they get pulled into that new struct.


Could you put these additional theorems in the appropriate files? It's annoying to have to rearrange the theorems after you are done. If you need additional `rat` theorems, add them to `rat/basic.lean`.


mkay, this might deserve a second (later) look.


I have deployed this commit :shipit:.


Actually, wouldn't have been 67dcbded10, since that was in an earlier release. So something post-5.0.11. Anyhow, fixed now.


Bluemix [toolchain](https://console-regional.ng.bluemix.net/devops/toolchains/f3786a65-725b-4f48-b29b-bbd351ba407c "myportfolio"): [Delivery Pipeline](https://console-regional.ng.bluemix.net/devops/pipelines/f610994a-2ee6-4f81-bd73-1fc38e67f2f3 "myportfolio") deployed [myportfolio](https://github.com/scowie/myportfolio/releases/tag/deploy-ibm-yp-us-south-cowiestephenjames-gmail.com-dev-20170808-005930 "deploy-ibm-yp-us-south-cowiestephenjames-gmail.com-dev-20170808-005930") to [dev](https://console.bluemix.net/apps/273910e5-9734-472a-b5b5-de2920264f74?env_id=ibm:yp:us-south "ibm:yp:us-south:cowiestephenjames@gmail.com:dev"), including this commit


```python
if roc_test < 0.8: sys.exit(1)
```
Is for Jenkins. It will signal a build fail when ROC area is too small


Should consider the GEO-IP round robin dns entry gridcoin.is.dopeshit.net as I update it regularly with both A and AAAA records. Also removing the remmed out IPv6 would be a smart idea , the ip stake is much more mature and iptables,ipfw or any firewall can handle ipv6 just the same as ipv4 and I have noticed as an ipv6 full node I get a vast number of spidered out connections via ipv6 it could benifit the network.

such as after the list of nodes a line such as
+echo "-=-=-=- Adding Backup GEO-IP Based Single Entry For All Nodes-=-=-=-"
+echo "addnode=gridcoin.is.dopeshit.net" | sudo tee -a $confign
+echo "-=-=-=- Creating config-=-=-=-"

It could be #remmed out by those whom do not want to use it in the script or removed if users do not want it as any other node , but the wiki list I personally update every 3 months , the and record gridcoin.is.dopeshit.net every few weeks if not at least every time a new  node goes on the wiki.


This change hasn't been deployed to our host and I don't have time to test it yet, but it works on my localhost.


We should be able to get away with `2016-present` to prevent the need for yearly changes


This cahnge killed MagicTelePortal plugin. :(


Credit to: [https://github.com/Tatwi](url)


Ah, makes sense!

So you should be able to pull the cookie even after a page refresh, correct?


![](https://github.trello.services/images/mini-trello-icon.png) [Обновить либы поддержки до 26 версии.](https://trello.com/c/r5DiL7oI/223-%D0%BE%D0%B1%D0%BD%D0%BE%D0%B2%D0%B8%D1%82%D1%8C-%D0%BB%D0%B8%D0%B1%D1%8B-%D0%BF%D0%BE%D0%B4%D0%B4%D0%B5%D1%80%D0%B6%D0%BA%D0%B8-%D0%B4%D0%BE-26-%D0%B2%D0%B5%D1%80%D1%81%D0%B8%D0%B8)


I will test for a while hyper as a sleep governor. Now it works more stable than before, since it was updated by Dorimanx.


[R/dEploidPlotly.R:26:1:](https://github.com/liuyingh/DEploid-r/blob/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/liuyingh/DEploid-r/blob/5334e70dda3683b7ef153a587bc49df0074feef0/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/liuyingh/DEploid-r/blob/5334e70dda3683b7ef153a587bc49df0074feef0/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/liuyingh/DEploid-r/blob/5334e70dda3683b7ef153a587bc49df0074feef0/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/5334e70dda3683b7ef153a587bc49df0074feef0/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


This is so much better. Thanks..


I've actually mis-targeted this comment, it was a thought re: copyright within a template, which was around user perception of an outdated website if the copyright year is not current.


[TagInput] 🔥 add separator, onChange, placeholder props (#1418)

Preview: documentation
Coverage: core | datetime


`iff` is hard to read anyway. Maybe just `only if` is clear and should be enough not to be misinterpreted (no one's going to wonder if we'll always reject on a name change).