runLIMMA: Differential expression analysis with LIMMA

In AlexanderKirchmair/datamisc: Various functions for data handling

Differential expression analysis with LIMMA

Description

Differential expression analysis with LIMMA

Usage

runLIMMA(
  data,
  design,
  formula = ~1,
  contrasts = NULL,
  trend = TRUE,
  robust = FALSE,
  p.adj.method = "fdr",
  do_log = FALSE,
  normalize = FALSE,
  norm.method = "vsn",
  ...
)

Arguments

data	Data
design	Experimental design/colData
formula	Formula
contrasts	Named list of contrasts, specified as c(factor, level, reflevel) or c(numeric)
trend	Trend
robust	Robust
p.adj.method	P.adj.method
do_log	Log-transform the data
normalize	Normalize
norm.method	Normalization method
...

Examples

data <- getTestData()
runLIMMA(log2(data$data+1), design = data$design, formula = ~ group + cov1, contrasts = data$contrasts)
runLIMMA(data$data, do_log = TRUE, design = data$design, formula = ~ group + cov1, contrasts = list(cov1 = "cov1"))

AlexanderKirchmair/datamisc documentation built on June 13, 2025, 5:26 a.m.