normaliseGeneExpression {psichomics}R Documentation

Filter and normalise gene expression

Description

Filter and normalise gene expression

Usage

normaliseGeneExpression(geneExpr, geneFilter = NULL, method = "TMM",
  p = 0.75, log2transform = TRUE, priorCount = 0.25)

Arguments

geneExpr

Matrix or data frame: gene expression

geneFilter

Boolean: filtered genes

method

normalization method to be used

p

percentile (between 0 and 1) of the counts that is aligned when method="upperquartile"

log2transform

Boolean: perform log2-transformation?

priorCount

Average count to add to each observation to avoid zeroes after log-transformation

Value

Gene expression filtered and normalised

Examples

geneExpr <- readFile("ex_gene_expression.RDS")
normaliseGeneExpression(geneExpr)

[Package psichomics version 1.9.1 Index]