normalizedExpression: Normalize gene expression to a normal reference for...

In JEFworks/badger: Bayesian approach for detecting copy number alterations from single cell RNA-seq data

Description

Normalize gene expression to a normal reference for expression-based karyotyping

Usage

normalizedExpression(mat, mat.ref, minMeanBoth = 4.5, minMeanTest = 6,
  minMeanRef = 8, verbose = TRUE)

Arguments

mat	Test gene expression matrix to be normalized
mat.ref	Normal reference gene expression matrix
minMeanBoth	Filter out genes with mean gene expression below this threshold in both samples. Default: 4.5
minMeanTest	Filter out genes with mean gene expression below this threshold in the test gene expression matrix. Default: 6
minMeanRef	Filter out genes with mean gene expression below this threshold in the reference gene expression matrix. Default: 8
verbose	Boolean for whether to print out verbose warnings. Default: TRUE

Value

List of two normalized gene expression matrices corresponding to mat and mat.ref

Examples

data('MM16.counts')
mat <- log2(MM16.counts + 1)
data('Normal.counts')
mat.ref <- log2(Normal.counts + 1)
mats <- normalizedExpression(mat, mat.ref)

JEFworks/badger documentation built on May 7, 2019, 7:40 a.m.