voomLimma: Perform the voom+limma procedure

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

Perform the voom+limma procedure

Description

Perform the voom+limma procedure

Usage

voomLimma(
  dgeList,
  design,
  contrasts,
  normalize.method = "none",
  block = NULL,
  correlation = NULL,
  weights = NULL,
  plot = FALSE,
  ...
)

Arguments

dgeList	A DGEList object, it should be ideally already filtered
design	The design matrix
contrasts	The contrast matrix
normalize.method	Character string, passed to voom, keep it none unless you are sure
block	Blocking factor, passed to voom
correlation	Correlation between duplicates, passed to voom
weights	Weights, passed to voom
plot	Logical, whether the variance-mean relationship should be ploted
...	Passed to eBayes

Value

MArrayLM object returned by eBayes, with voom object in the voom element of the list

Examples

y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4)
d <- edgeR::DGEList(counts=y, group=rep(1:2,each=2))
d <- edgeR::calcNormFactors(d)
design <- model.matrix(~gl(2,2))
colnames(design) <- c("baseline", "treatment")
contrasts <- limma::makeContrasts("treatment", levels=design)
dvl <- voomLimma(d, design=design, contrasts=contrasts)

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