data_norm: Subset, Log2 transform and normalizes data.

In sdrowland/RSMod: Creates a 2D or 3D mapping of RNA-Seq Data

Usage

data_norm(trans, sub)

Arguments

trans
sub

Examples

##---- 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)
  }

sdrowland/RSMod documentation built on July 17, 2021, 7:16 p.m.