runLimma: DEG Analysis with Limma

In yduan004/signatureSearchData: Datasets for signatureSearch package

DEG Analysis with Limma

Description

This function runs DEG analysis with Limma at user defined FDR and LFC cutoff by providing CMAP02 normalized expression values and annotation of treatment v.s. control samples. For more context of the CMAP02 database, please consult the vignette of this package.

Usage

runLimma(df, comp_list, fdr = 0.05, foldchange = 1, verbose = TRUE)

Arguments

df	data.frame containing normalized intensity values of CMAP02 samples
comp_list	list of CEL file ids of treatment and control samples for each compound treatment. The list for CMAP02 data is generated from the sampleList function.
fdr	cutoff of false discovery rate (FDR) for defining DEGs
foldchange	cutoff of log2 fold change (LFC) for defining DEGs
verbose	TRUE or FALSE

Value

list containing DEGs and log2FC matrix

Examples

path <- system.file("extdata", "cmap_instances_02.txt", package="signatureSearchData")
cmap_inst <- read.delim(path, check.names=FALSE) 
comp_list <- sampleList(cmap_inst, myby="CMP_CELL")
df <- as.data.frame(matrix(runif(70), ncol=7))
colnames(df) <- unlist(comp_list[1])
degList <- runLimma(df, comp_list[1])  

yduan004/signatureSearchData documentation built on April 7, 2023, 4:12 a.m.