Make a combined data matrix from cuffdiff output for gene-level data

makeCuffDiffMatrix.R

makeCuffDiffMatrix <- function(directory='.') {
  m = read.delim(file.path(directory,'genes.fpkm_tracking'),header=TRUE)
  d = read.delim(file.path(directory,'gene_exp.diff'),header=TRUE)
  x = seq(1,nrow(d),nrow(m))
  dt1 = m
  for(i in 1:length(x)) {
    dt = d[x[i]:(x[i]+nrow(m)-1),]
    dt$fdr=p.adjust(dt$p_value,method='fdr')
    colnames(dt)=paste(dt[1,4],dt[1,5],colnames(dt),sep="_")
    dt1 = cbind(dt1,dt[,-c(1:5,7,8)])
  }
  return(dt1)
}