diff --git a/R/preprocessing.R b/R/preprocessing.R index efc1ee5..625fa54 100644 --- a/R/preprocessing.R +++ b/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") } diff --git a/inst/example/preproc_dpclust_master_file.R b/inst/example/preproc_dpclust_master_file.R index 65fc21e..1c25a7e 100644 --- a/inst/example/preproc_dpclust_master_file.R +++ b/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)) { diff --git a/man/ascatNgsToBattenberg.Rd b/man/ascatNgsToBattenberg.Rd index 267e379..0310280 100644 --- a/man/ascatNgsToBattenberg.Rd +++ b/man/ascatNgsToBattenberg.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/preprocessing.R +% Please edit documentation in R/copynumber.R \name{ascatNgsToBattenberg} \alias{ascatNgsToBattenberg} \title{Transform ASCAT NGS output into Battenberg} diff --git a/man/ascatToBattenberg.Rd b/man/ascatToBattenberg.Rd index dac728b..bb77603 100644 --- a/man/ascatToBattenberg.Rd +++ b/man/ascatToBattenberg.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/preprocessing.R +% Please edit documentation in R/copynumber.R \name{ascatToBattenberg} \alias{ascatToBattenberg} \title{Transform ASCAT output into Battenberg} diff --git a/man/createProjectFile.Rd b/man/createProjectFile.Rd index ae72872..82212b6 100644 --- a/man/createProjectFile.Rd +++ b/man/createProjectFile.Rd @@ -4,9 +4,10 @@ \alias{createProjectFile} \title{Creates a DPClust project master file} \usage{ -createProjectFile(outputfile, donornames, samplenames, purities, sex, - datafiles = paste(samplenames, "_allDirichletProcessInfo.txt", sep = ""), - cndatafiles = NULL, indeldatafiles = NULL) +createProjectFile(outputfile, donornames, samplenames, sex, purities = NULL, + rho_and_psi_files = NULL, datafiles = paste(samplenames, + "_allDirichletProcessInfo.txt", sep = ""), cndatafiles = NULL, + indeldatafiles = NULL) } \arguments{ \item{outputfile}{Full path with filename where the output will be written} @@ -15,15 +16,15 @@ createProjectFile(outputfile, donornames, samplenames, purities, sex, \item{samplenames}{A vector with sample identifiers} -\item{purities}{A vector with a purity value per sample} - \item{sex}{A vector with the sex of each donor} +\item{purities}{A vector with a purity value per sample} + \item{datafiles}{Vector with filenames in which the DPClust input is contained (Default: [samplename]_allDirichletProcessInfo.txt)} -\item{indeldatafiles}{A vector with indel DPClust input files (Default: NULL)} +\item{cndatafiles}{A vector with CNA DPClust input files (Default: NULL)} -\item{cnadatafiles}{A vector with CNA DPClust input files (Default: NULL)} +\item{indeldatafiles}{A vector with indel DPClust input files (Default: NULL)} } \description{ Creates a DPClust project master file diff --git a/man/load.data.Rd b/man/load.data.Rd deleted file mode 100644 index c84b6eb..0000000 --- a/man/load.data.Rd +++ /dev/null @@ -1,49 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/LoadData.R -\name{load.data} -\alias{load.data} -\title{THIS FUNCTION IS DEPRECATED - SHOULD BE MERGED WITH THE ONE IN DPCLUST} -\usage{ -load.data(datpath, samplename, list_of_data_files, cellularity, Chromosome, - position, WT.count, mut.count, subclonal.CN, no.chrs.bearing.mut, - mutation.copy.number, subclonal.fraction, data_file_suffix) -} -\arguments{ -\item{datpath}{Path to where the input datafiles can be found, type string.} - -\item{samplename}{A unique identifier for this particular individual/experiment, type string.} - -\item{list_of_data_files}{A list of file names that are available in datpath, list of strings.} - -\item{cellularity}{Vector containing the cellularity estimate for each sample in this set, vector of floats.} - -\item{Chromosome}{The name of the column containing the chromosome information in the input, type string.} - -\item{position}{The name of the column containing the position information in the input, type string.} - -\item{WT.count}{The name of the column containing the wild type allele count information in the input, type string.} - -\item{mut.count}{The name of the column containing the mutation allele count information in the input, type string.} - -\item{subclonal.CN}{The name of the column containing the total subclonal copynumber information in the input, type string.} - -\item{no.chrs.bearing.mut}{The name of the column containing the number of chromsomes bearing the mutation information in the input, type string.} - -\item{mutation.copy.number}{Mutation copy number} - -\item{subclonal.fraction}{Subclonal fraction} - -\item{data_file_suffix}{A suffix to be appended to each item in list_of_data_files to complete the filenames (for example dirichletInput.R), type string.} -} -\value{ -A named list of matrices and vectors with the following items: chromosome, position, WTCount, mutCount, totalCopyNumber, copyNumberAdjustment, non.deleted.muts, kappa, mutation.copy.number, subclonal.fraction, removed_indices, chromosome.not.filtered, mut.position.not.filtered -} -\description{ -load.data -} -\details{ -Load data files for a specific set of samples belonging to the same individual/experiment. -} -\author{ -sd11 -}