limma_deg: Differential Gene Expression Analysis by Limma

In psychemistz/ovltools: Tools for estimating distribution overlap between two sample distributions

Differential Gene Expression Analysis by Limma

Description

utility function to get differential expression table from limma function in limma package.

Usage

limma_deg(gex, label)

Arguments

gex	A gene x sample data frame. rownames are gene or probe ids and colnames are sample ids.
label	A factor. Indicates class label of samples. It should be ordered as sample ids in gex data frame.

Value

DEG data frame which contains logFC, AveExpr, t, P.Value, adj.P.Val (by Benjamin-Hochberg correction)

Author(s)

Seongyong Park (2020-08-18)

Examples

gex = do.call(rbind, lapply(1:100, function(i) rnorm(100, sample(1:10), 2)))
rownames(gex) = paste0("gid", 1:100)
colnames(gex) = paste0("sid", 1:100)
label = factor(c(rep("ALL", 50), rep("AML", 50)), levels=c("ALL", "AML"))
head(limma_deg(gex, label))

psychemistz/ovltools documentation built on April 1, 2022, 2:26 a.m.