R/inputToTSS.R

In BrendelGroup/TSRchitect: Promoter identification from large-scale TSS profiling data

#' @title \strong{inputToTSS}
#' @description \code{inputToTSS} extracts TSS information from each
#' attached .bam or .bed file in a tssObject object
#'
#' @param experimentName an S4 object of class tssObject with bam files loaded
#'
#' @return produces a \linkS4class{GRangesList} containing separate
#' \linkS4class{GRanges} objects for each .bam file contained within
#' \emph{experimentName}, placing them them in the returned \emph{tssObject}.
#' 
#' @import BiocGenerics
#' @importFrom GenomicRanges granges GRanges GRangesList
#' @importFrom GenomeInfoDb sortSeqlevels
#' @importFrom IRanges IRanges
#' @importFrom S4Vectors first second split
#'
#' @examples
#' load(system.file("extdata", "tssObjectExample.RData",
#' package="TSRchitect"))
#' tssObjectExample <- inputToTSS(experimentName=tssObjectExample)
#'
#' @note An example similar to the one provided can be
#' found in the vignette (/inst/doc/TSRchitect.Rmd).
#'
#' @export
#' @rdname inputToTSS-methods


setGeneric("inputToTSS",
    function(experimentName)
    standardGeneric("inputToTSS")
)

#' @rdname inputToTSS-methods

setMethod("inputToTSS",
          signature(experimentName="tssObject"),
          function(experimentName) {
            message("... inputToTSS ...")
            if (length(experimentName@bamDataFirstRead)>0) {
              message("\nBeginning input to",
                      " TSS data conversion ...\n\n")
              bam.len <- length(experimentName@bamDataFirstRead)
              bam.vec <- vector(mode="list", length=bam.len)
              bam.gr <- lapply(experimentName@bamDataFirstRead, granges, use.names=TRUE, use.mcols=TRUE)
              for (i in 1:bam.len) {
                message("Retrieving data from bam file #", i, "...\n\n")
                this.gr <- bam.gr[[i]]
                gr.list <- S4Vectors::split(this.gr, strand(this.gr))
                gr.plus <- gr.list$'+'
                gr.minus <- gr.list$'-'
                gr1 <- GRanges(seqnames=seqnames(gr.plus),
                               ranges=IRanges(
                                 start=start(gr.plus),
                                 end=start(gr.plus)
                                 ),
                               strand=strand(gr.plus)
                              )
                gr2 <- GRanges(seqnames=seqnames(gr.minus),
                               ranges=IRanges(
                                 start=end(gr.minus),
                                 end=end(gr.minus)
                                 ),
                               strand=strand(gr.minus)
                              )
                gr.combined <- c(gr1,gr2)
                gr.combined <- sortSeqlevels(gr.combined)
                gr.combined <- sort(gr.combined)
                bam.vec[[i]] <- gr.combined
              }
              GR.list <- GRangesList(bam.vec)
              experimentName@tssTagData <- GR.list
              experimentName@tssCountData <- vector(mode="list", length=bam.len)
              message("Done. TSS data from ", bam.len, " separate bam files" ,
                      " have been successfully\nadded to the tssObject.\n\n")
              message("----------------------------------------------------\n")
            }
            if (length(experimentName@bedData)>0) {
              message("\nBeginning input to",
                      " TSS data conversion ...\n\n")
              if (class(experimentName@bedData[[1]])=="GRanges") { #i.e bed single-end
                bed.len <- length(experimentName@bedData)
                bed.vec <- vector(mode="list", length=bed.len)
                bed.gr <- experimentName@bedData
                for (i in 1:bed.len) {
                  message("Retrieving data from bed file #", i, "...\n\n")
                  this.gr <- bed.gr[[i]]
                  gr.list <- S4Vectors::split(this.gr, strand(this.gr))
                  gr.plus <- gr.list$'+'
                  gr.minus <- gr.list$'-'
                  gr1 <- GRanges(seqnames=seqnames(gr.plus),
                                 ranges=IRanges(
                                          start=start(gr.plus),
                                          end=start(gr.plus)
                                        ),
                                 strand=strand(gr.plus)
                                )
                  gr2 <- GRanges(seqnames=seqnames(gr.minus),
                                 ranges=IRanges(
                                          start=end(gr.minus),
                                          end=end(gr.minus)
                                        ),
                                 strand=strand(gr.minus)
                                )
                  gr.combined <- c(gr1,gr2)
                  gr.combined <- sortSeqlevels(gr.combined)
                  gr.combined <- sort(gr.combined)
                  bed.vec[[i]] <- gr.combined
                }
                if (exists("bam.len")==TRUE) {
                  combined.len <- bam.len+bed.len
                  start.pos <- bam.len+1
                  combined.vec <- vector(mode="list", length=combined.len)
                  combined.vec[1:bam.len] <- bam.vec
                  combined.vec[start.pos:combined.len] <- bed.vec
                  GR.list <- GRangesList(combined.vec)
                  experimentName@tssTagData <- GR.list
                  experimentName@tssCountData <- vector(mode="list", length=combined.len)
                } else {
                  GR.list <- GRangesList(bed.vec)
                  experimentName@tssTagData <- GR.list
                  experimentName@tssCountData <- vector(mode="list", length=bed.len)
                }
                GR.list <- GRangesList(bed.vec)
                experimentName@tssTagData <- GR.list
                experimentName@tssCountData <- vector(mode="list", length=bed.len)
                message("Done. TSS data from ", bed.len, " separate bed files" ,
                        " have been successfully\nadded to the tssObject.\n\n")
                message("----------------------------------------------------\n")
              }
              if (class(experimentName@bedData[[1]])=="Pairs") { #i.e. bed paired-end (bedpe)
                bedpe.len <- length(experimentName@bedData)
                bedpe.vec <- vector(mode="list", length=bedpe.len)
                bed.gr <- lapply(experimentName@bedData, first)
                for (i in 1:bedpe.len) {
                  message("Retrieving data from bedpe file #", i, "...\n\n")
                  this.gr <- bed.gr[[i]]
                  gr.list <- S4Vectors::split(this.gr, strand(this.gr))
                  gr.plus <- gr.list$'+'
                  gr.minus <- gr.list$'-'
                  gr1 <- GRanges(seqnames=seqnames(gr.plus),
                                 ranges=IRanges(
                                          start=start(gr.plus),
                                          end=start(gr.plus)
                                        ),
                                 strand=strand(gr.plus)
                                )
                  gr2 <- GRanges(seqnames=seqnames(gr.minus),
                                 ranges=IRanges(
                                          start=end(gr.minus),
                                          end=end(gr.minus)
                                        ),
                                 strand=strand(gr.minus)
                                )
                  gr.combined <- c(gr1,gr2)
                  gr.combined <- sortSeqlevels(gr.combined)
                  gr.combined <- sort(gr.combined)
                  bedpe.vec[[i]] <- gr.combined
                }
                GR.list <- GRangesList(bedpe.vec)
                if (exists("bam.len")==TRUE) {
                  combined.len <- bam.len+bedpe.len
                  start.pos <- bam.len+1
                  combined.vec <- vector(mode="list", length=combined.len)
                  combined.vec[1:bam.len] <- bam.vec
                  combined.vec[start.pos:combined.len] <- bedpe.vec
                  GR.list <- GRangesList(combined.vec)
                  experimentName@tssTagData <- GR.list
                  experimentName@tssCountData <- vector(mode="list", length=combined.len)
                } else {
                  GR.list <- GRangesList(bedpe.vec)
                  experimentName@tssTagData <- GR.list
                  experimentName@tssCountData <- vector(mode="list", length=bedpe.len)
                }
                message("Done. TSS data from ", bedpe.len, " separate bed files" ,
                        " have been successfully\nadded to the tssObject.\n\n")
                message("----------------------------------------------------\n")
              }
            }
            message(" Done.\n")
            return(experimentName)
          }
         )