voomSVA: Run SVA on a count matrix transformed by voom

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

Run SVA on a count matrix transformed by voom

Description

Run SVA on a count matrix transformed by voom

Usage

voomSVA(object, design, ...)

## S4 method for signature 'matrix,matrix'
voomSVA(object, design)

## S4 method for signature 'DGEList,matrix'
voomSVA(object, design)

## S4 method for signature 'DGEList,formula'
voomSVA(object, design)

Arguments

object	A count matrix
design	Design matrix or formula
...	Other parameters

Value

SV matrix

Methods (by class)

• voomSVA(object = matrix, design = matrix): Method for count matrix and design matrix

• voomSVA(object = DGEList, design = matrix): Method for DGEList and design matrix

• voomSVA(object = DGEList, design = formula): Method for count matrix and design formula

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))
voomSVA(exCounts, design=exDesign)

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