Pre-processing gene expression matrix

Use this function to perform a number of pre-processing steps, including log transformation, normalization and standardization of gene expression matrix. NOTE: If multiple options are set true, the sequence of pre-processing steps performed are variance filtering, log2 transformation, upper quantile normalization and standardization.

pre.process(gex, var.filter = TRUE, log = FALSE, UQ = FALSE,
  std = TRUE)

Arguments

gex

a gene expression matrix with genes in columns and samples in rows
var.filter

logical. specify whether genes are filtered based on variance. Default = TRUE
log

logical. specify whether log2(x+1) transformation should be performed. Default = FALSE
UQ

logical. specify whether upper quantile normalization should be performed. Default = FALSE
scale

logical. specifiy whether standardization should be performed. Default = TRUE

Value

a processed gene expression matrix

Examples

Proc.GA.pcg <- pre.process(GA.pcg)