function addMedipsEnrichmentFactors() terminates with error

[anjalisa]

Hello,

Running the function makeQset() with the parameter set CNVmethod = "qseaPooled" , coverageMethod = "qseaPaired" works smoothly until function addMedipsEnrichmentFactors() is reached.
Error occurs at the following lines within the function addMedipsEnrichmentFactors() :

enrichDataMeCap <- parallel::mclapply(pulldownFileNames,
                                       function(x){
                                       calculateCpGEnrichment(x, BSgenome, exportPath = exportPath,
                                                           extend = extend, shift = shift, uniq = uniq,
                                                           chr.select = chr.select, paired = paired)
                                  }, mc.cores = nCores) %>%
  do.call(rbind, . )
 
qseaSet@sampleTable <- qsea::getSampleTable(qseaSet) %>%  
   dplyr::bind_cols(dplyr::select(enrichDataMeCap,-file))

The parallelisation with mclapply() somehow does not seem to run smoothly all the time.
Additionally, it states that dplyr::select can't be applied to a matrix.

[SPPearce]

Hi Anja,

Thank you for the bug report and the pull request to try and fix it, very much appreciated!
I'll take a look at the PR tomorrow, but just from a quick look at this function I think it needs the arguments checking (it has paired = TRUE being set by default for instance, which will probably mean it fails on single-ended reads too.

[SPPearce]

I think this has been fixed now, in the new version we have just released.