voomRemoveSV: Apply SVA to voom-transformed count data, and return the voom...

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Apply SVA to voom-transformed count data, and return the voom expression matrix with surrogate variables' effect removed

Description

Apply SVA to voom-transformed count data, and return the voom expression matrix with surrogate variables' effect removed

Usage

voomRemoveSV(counts, designMatrix)

Arguments

counts	A matrix of counts
designMatrix	Design matrix

Value

The voom expression matrix, with SV effects removed

Examples

exCounts <- matrix(rpois(12000, 10), nrow=2000, ncol=6)
exCounts[1:100, 2:3] <- exCounts[1:100,2:3]+20
exDesign <- model.matrix(~gl(2,3))
head(voomRemoveSV(exCounts, designMatrix=exDesign))
## compare the results without SV removal, note the values in the 
## second and third column are much larger than the rest
head(voom(exCounts, exDesign)$E)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.