countsSVA: Apply SVA to transformed count data

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

Apply SVA to transformed count data

Description

Apply SVA to transformed count data

Usage

countsSVA(
  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
...	Passed to inferSV

Value

The SV matrix

Examples

set.seed(1887)
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))
countsSVA(exCounts, designMatrix=exDesign)

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