Exclude genes without a value over 2rpkm and select only columns marching string "rpkm"

rpkm.R

source("http://bioconductor.org/biocLite.R")
biocLite("preprocessCore")
library(preprocessCore)
data <- read.delim(gzfile("fileOfInterest.txt.gz"), sep="\t")
data <- data[,grep("RPKM", colnames(data))]
filtered <- data[!apply(data, 1, function(x){ all(x <2) }),]
qn <- normalize.quantiles(as.matrix(filtered), copy = TRUE)]
qn <- as.data.frame(qn)
colnames(qn) <- colnames(filtered)
rownames(qn) <- rownames(filtered)