pre.process: Pre-processing gene expression matrix

In aritronath/iMIRAGE: iMIRAGE: imputed miRNA activity from gene expression (Title Case)

Description

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.

Usage

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)

aritronath/iMIRAGE documentation built on Dec. 29, 2019, 1:28 a.m.