#' Load Fcount output from : DEXSeq_after_Fcount.R into DEXSeq
#' Copyright 2015 Vivek Bhardwaj (bhardwaj@ie-freiburg.mpg.de). Licence: GPLv3.
#' Read Fcount output and convert to dxd
#'
#' @export
DSFromFC <- function(countFile){
# Take a fcount file and convert it to dcounts for dexseq
message("Reading and adding Exon IDs for DEXSeq")
fc <- read.table(countFile,,head=T,skip = 1)
fc <- dplyr::arrange(fc, Geneid,Chr,Start)
dcounts <- dplyr::select(fc,-c(2:6))
id <- as.character(dcounts[,1])
n <- id
split(n,id) <- lapply(split(n ,id), seq_along )
rownames(dcounts) <- sprintf("%s%s%03.f",id,":E",as.numeric(n))
dcounts <- dcounts[,2:ncol(dcounts)]
dcounts <- dcounts[substr(rownames(dcounts), 1, 1) != "_", ] #remove _ from beginnning of gene name
## get genes and exon names out
splitted <- strsplit(rownames(dcounts), ":")
exons <- sapply(splitted, "[[", 2)
genesrle <- sapply(splitted, "[[", 1)
list(dcounts=dcounts,exons=exons,genesrle=genesrle)
}
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