R/cufflinks.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

###########################################################################/**
# @RdocDefault cufflinks
#
# @title "Calls cufflinks on input bam file(s)"
#
# \description{
#  @get "title".
# }
#
# @synopsis
#
# \arguments{
#   \item{bams}{Vector of pathnames (.sam or .bam)}
#   \item{optionsVec}{Vector of named options}
#   \item{...}{...}
#   \item{commandName}{Name of executable}
#   \item{verbose}{See @see "R.utils::Verbose".}
# }
#
# @author "TT"
#
# @keyword internal
#*/###########################################################################
setMethodS3("cufflinks", "default", function(bams=NULL,  ## vector of pathnames
                                             optionsVec, ## vector of named options
                                             ...,
                                             commandName='cufflinks',
                                             verbose=FALSE) {

  ## ( Support a call like this: "cufflinks <options> bams" )

  # Argument 'bams'
  bams <- Arguments$getReadablePathnames(bams)
  assertNoDuplicated(bams)
  cufflinksArgs <- bams

  ## Add dashes as appropriate to names of "cufflinks options"
  cufflinksOptions <- optionsVec
  nms <- names(optionsVec)
  names(cufflinksOptions) <- paste(ifelse(nchar(nms) == 1, "-", "--"), nms, sep="")

  res <- do.call(what=systemCufflinks, args=list(commandName=commandName, args=c(cufflinksOptions, cufflinksArgs)))

  res
}) # cufflinks()