[R/DEploidR.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Extract read counts from tab-delimited text files of a single sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The allele count files must be tab-delimited. The allele count files contain three columns: chromosomes, positions and allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:11:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:20:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:20:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                   ^
```
[R/DEploidR.R:20:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:20:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/DEploidR.R:23:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L23) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( data.frame( CHROM = ref[, 1],
           ^
```
[R/DEploidR.R:35:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The VCF file should only contain one sample. If more samples present in the VCF, it only returns coverage for of the first sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:39:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
#' @param ADFieldIndex Index of the AD field of the sample field. For example, if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:41:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:49:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:49:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                   ^
```
[R/DEploidR.R:49:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:49:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:57:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L57) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:61:13:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L61) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:73:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L73) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:79:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L79) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:81:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L81) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:82:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L82) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:84:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L84) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( data.frame( CHROM = vcf[, 1],
           ^
```
[R/DEploidR.R:96:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The text file must have header, and population level allele frequency recorded in the "PLAF" field.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:105:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L105) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:108:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
^~~~~~~~~~~
```
[R/DEploidR.R:108:25:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractPLAF <- function ( plafFileName ){
                        ^
```
[R/DEploidR.R:108:27:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
                          ^~~~~~~~~~~~
```
[R/DEploidR.R:109:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L109) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( read.table(plafFileName, header = T)$PLAF )
           ^
```
[R/DEploidR.R:115:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L115) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the MCMC samples of the proportion, indexed by the MCMC chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:117:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportions Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:130:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:131:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
#' panelFile = system.file("extdata", "labStrains.test.panel.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:137:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
#' plotProportions( PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions" )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L139) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function (proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:29:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L139) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotProportions <- function (proportions, title = "Components",
                            ^
```
[R/DEploidR.R:140:24:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                       ^~~~~~~
```
[R/DEploidR.R:140:37:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                    ^~~~~~~~
```
[R/DEploidR.R:140:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                  ^~~~~~~~
```
[R/DEploidR.R:141:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L141) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot alternative allele count vs reference allele count at each site.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:159:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
#' @param exclude.ref Numeric array of reference allele count at sites that are not deconvoluted.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:161:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
#' @param exclude.alt Numeric array of alternative allele count at sites that are not deconvoluted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:183:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L183) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:183:26:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L183) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
                         ^
```
[R/DEploidR.R:184:21:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:184:40:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:185:21:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                    ^~~~~~~
```
[R/DEploidR.R:185:34:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                 ^~~~~~~~
```
[R/DEploidR.R:185:48:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                               ^~~~~~~~
```
[R/DEploidR.R:189:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L189) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:190:10:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L190) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    plot ( ref, alt, xlim = c(0, tmpRange), ylim = c(0, tmpRange),
         ^
```
[R/DEploidR.R:232:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L232) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:239:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:243:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:243:22:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                     ^
```
[R/DEploidR.R:243:24:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                       ^~~~~~~
```
[R/DEploidR.R:245:17:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                ^~~~~~~
```
[R/DEploidR.R:245:30:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                             ^~~~~~~~
```
[R/DEploidR.R:245:44:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                           ^~~~~~~~
```
[R/DEploidR.R:246:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:248:9:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L248) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:250:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L250) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (hist(obsWSAF[tmpWSAFIndex], main = title,
           ^
```
[R/DEploidR.R:263:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L263) *style:* **Lines should not be more than 80 characters.**
```r
#' @param obsWSAF Numeric array of observed altenative allele frequencies within sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:282:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:283:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:290:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L290) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:291:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L291) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:295:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:295:28:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                           ^
```
[R/DEploidR.R:295:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                   ^~~~~~~
```
[R/DEploidR.R:295:45:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                            ^~~~~~~
```
[R/DEploidR.R:297:23:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:297:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:297:50:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:298:10:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L298) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    plot ( plaf, obsWSAF, cex = 0.5, xlim = c(0, 1), ylim = c(0, 1),
         ^
```
[R/DEploidR.R:302:16:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L302) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
        points ( plaf, expWSAF, cex = 0.5, col = "blue")
               ^
```
[R/DEploidR.R:310:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot observed alternative allele frequency within sample against expected WSAF.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:329:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L329) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:330:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L330) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:331:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L331) *style:* **Lines should not be more than 80 characters.**
```r
#' PG0390CoverageVcf.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-noPanel"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:332:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L332) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageVcf.deconv$Proportions[dim(PG0390CoverageVcf.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:336:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:336:28:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                           ^
```
[R/DEploidR.R:336:29:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                            ^~~~~~~
```
[R/DEploidR.R:336:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                                     ^~~~~~~
```
[R/DEploidR.R:338:23:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:338:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:338:50:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:350:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L350) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Compute observed allele frequency within sample from the allele counts.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:367:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L367) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:372:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L372) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:374:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L374) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function (alt, ref) {
^~~~~~~~~~~~~~
```
[R/DEploidR.R:374:28:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L374) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
computeObsWSAF <- function (alt, ref) {
                           ^
```
[R/DEploidR.R:375:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L375) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( alt / (ref + alt + 0.00000001) )
           ^
```
[R/DEploidR.R:381:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L381) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the posterior probabilities of a haplotype given the refernece panel.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:383:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
#' @param posteriorProbabilities Posterior probabilities matrix with the size of number of loci by the number of reference strain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:30:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                             ^
```
[R/DEploidR.R:391:31:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                              ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:67:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:392:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L392) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/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/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


Kek thanks


The omition of the protocol part in the "Location:" header broke the functionality of indexing in typo3solr via file_get_contents()
By removing line 104 and line 105 we were able to fix the behaviour, but I am not sure why this was introduced in the first place. Could you please explain?

Thank you very much!
Hendrik


We should probably conform to the same pattern in the rest of the library and use the commented out part instead of 35-39.