countsRemoveSV: Apply SVA to transformed count data and return the...

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

Apply SVA to transformed count data and return the transformed matrix removing the effect of surrogate variables

Description

Apply SVA to transformed count data and return the transformed matrix removing the effect of surrogate variables

Usage

countsRemoveSV(
  counts,
  designMatrix,
  transformFunc = function(counts, designMatrix) voom(counts, designMatrix)$E
)

Arguments

counts	A matrix of counts
designMatrix	Design matrix
transformFunc	A function to transform the count data

Value

The 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(countsRemoveSV(exCounts, designMatrix=exDesign))

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