Update package documentation and small fix in dpclust master file pip…

…eline

R/preprocessing.R

@@ -734,7 +734,7 @@ addVcfInfoCol = function(vcf, data, number, type, description, abbreviation) {
 #' @param purities A vector with a purity value per sample
 #' @param sex A vector with the sex of each donor
 #' @param datafiles Vector with filenames in which the DPClust input is contained (Default: [samplename]_allDirichletProcessInfo.txt)
-#' @param cnadatafiles A vector with CNA DPClust input files (Default: NULL)
+#' @param cndatafiles A vector with CNA DPClust input files (Default: NULL)
 #' @param indeldatafiles A vector with indel DPClust input files (Default: NULL)
 #' @author sd11
 #' @export
@@ -768,7 +768,7 @@ createProjectFile = function(outputfile, donornames, samplenames, sex, purities=
                       datafile=datafiles, 
                       cellularity=purities, 
                       sex=sex, 
-                      cnadatafile=ifelse(!is.null(cnadatafiles), cnadatafiles, NA),
+                      cnadatafile=ifelse(!is.null(cndatafiles), cndatafiles, NA),
                       indeldatafiles=ifelse(!is.null(indeldatafiles), indeldatafiles, NA), stringsAsFactors=F)
   write.table(output, file=outputfile, quote=F, row.names=F, sep="\t")
 }

inst/example/preproc_dpclust_master_file.R

@@ -18,9 +18,9 @@ option_list = list(
 opt_parser = OptionParser(option_list=option_list)
 opt = parse_args(opt_parser)
 
-donornames = strsplit(opt$donornames, ",")
-samplenames = strsplit(opt$samplenames, ",")
-sex = strsplit(opt$sex, ",")
+donornames = unlist(strsplit(opt$donornames, ","))
+samplenames = unlist(strsplit(opt$samplenames, ","))
+sex = unlist(strsplit(opt$sex, ","))
 outputfile = opt$output
 
 if (!is.null(opt$rho_and_psi)) {