View source: R/Clustering_Sinha.R
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (trans, sub)
{
names = colnames(trans[2:ncol(trans)])
colnames(trans) = c("itag", names)
if (!(missing(sub))) {
colnames(sub) = c("itag")
data3 = data[which(trans$itag %in% sub$itag), ]
rownames(data3) = data3$itag
data3 = data3[, c(2:ncol(data3))]
}
if (missing(sub)) {
data3 = data
rownames(data3) = data3$itag
data3 = data3[, c(2:ncol(data3))]
}
countsadj = log2(data3)
countsadj = as.matrix(countsadj)
countsadj[is.infinite(countsadj)] = 0
countsadj[is.na(countsadj)] = 0
norm.data = data.Normalization(countsadj, type = "n1", normalization = "row")
norm.data[is.na(norm.data)] = 0
norm.data[is.infinite(norm.data)] = 0
return(norm.data)
}
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