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#' Import from FeatureCounts
#'
#' This functions imports the output from FeatureCounts
#'
#' FeatureCounts produces two files, the txt that contain the expression values and then the summary that containts
#' all the information about the mapping statistics. This function imports both and stores them in a corresponding list.
#'
#' @param file Character, file name
#' @param skip Number of lines to skip from txt file
#' @param headerLine Linenumber that contains the header information
#'
#' @return A list with expValues, geneInfo and summary
#'
#' @author Daniel Fischer
#'
#' @examples
#'
#' # Define here the location on HDD for the example file
#' fpath <- system.file("extdata","featureCountsExample.txt", package="GenomicTools.fileHandler")
#' # Import the example featureCounts file
#' fcFile <- importFeatureCounts(file=fpath)
#'
#' @export
importFeatureCounts <- function(file, skip=0, headerLine=2){
tmp <- read.table(file, header=TRUE, stringsAsFactors=FALSE, skip=skip)
# If we skip some of the head, we might cut off the header, so I import it here again.
if(skip>0){
header <- read.table(file, header=FALSE, stringsAsFactors=FALSE, skip=headerLine-1, nrows = 1)
colnames(tmp) <- header
}
expValues <- tmp[,c(1,7)]
geneInfo <- tmp[,1:6]
tmp <- read.table(paste(file,".summary",sep=""), header=TRUE, stringsAsFactors=FALSE)
result <- list(expValues=expValues, geneInfo=geneInfo, summary=tmp)
class(result) <- "featureCounts"
result
}
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