R/easyRNASeq-BamParam.R

In easyRNASeq: Count summarization and normalization for RNA-Seq data

#' BamParam constructor
#'
#' This constructs a \code{\linkS4class{BamParam}} object.
#' The default parameters are derived from the currently most
#' common RNA-Seq experimental use-case and are detailed below:
#' \itemize{
#' \item paired is TRUE, \emph{i.e.} paired-end sequencing is expected.
#' \item stranded is FALSE \emph{i.e.} stranded sequencing is not expected.
#' \item yieldSize is set to 1,000,000. This is the amount of reads iteratively
#' processed from the bam file stream. It is a compromise between speed,
#' process-parallelization and memory usage.
#' }
#'
#' Calling the constructor without argument result in the
#' default parameter described above to be returned. Calling
#' the constructor with any  parameter will affect the value
#' of the selected parameters, leaving the other parameters
#' unaffected.
#'
#' @aliases BamParam BamParam,ANY-method
#' @name easyRNASeq BamParam constructor
#' @rdname easyRNASeq-BamParam
#' @param paired boolean whether the BAM file contains paired-end data or not
#' @param stranded boolean whether the reads are strand specific
#' @param strandProtocol factor with values 'reverse' and 'forward' specifying the
#' type of strand specificity protocol. 'reverse', the reads are on the opposite
#' strand to the gene; typical for Illumina TRUSEQ strand-specific protocol.
#' @param yieldSize the amount of reads to be streamed at a time. Default to 1M
#' @examples
#' # the defaults
#' BamParam()
#'
#' # change the default
#' BamParam(paired=FALSE)
#' BamParam(stranded=TRUE,yieldSize=1L)
#' BamParam(stranded=TRUE,strandProtocol="forward",yieldSize=1L)
#'
setMethod(f="BamParam",
          signature="ANY",
          definition=function(
                              paired=TRUE,
                              stranded=FALSE,
                              strandProtocol=c("reverse","forward"),
                              yieldSize=1e6L){
              strandProtocol <- match.arg(strandProtocol)
              new("BamParam",
                  paired=paired,
                  stranded=stranded,
                  strandProtocol=strandProtocol,
                  yieldSize=yieldSize)
          })