diff_limma_all: diff_limma_all (from limma functions).

In ShirinG/exprAnalysis: A package for analysing RNA-seq and expression array data

Description

This calculates the differentially expressed genes among all group comparisons.

Usage

diff_limma_all(expmatrix, design, groupcomparisons, p.value = 0.05,
  lfc = log2(1.5), projectfolder = getwd())

Arguments

expmatrix	An input matrix with gene names as row names and sample names as column names.
design	Binary design matrix of samples' treatment groups.
groupcomparisons	Group comparisons for differential expression analysis.
p.value	Significance threshold. Defaults to 0.05
lfc	Log fold change threshold. Defaults to 1.5
projectfolder	File path where to save the output to. Defaults to working directory. Here, it saves the output to a subfolder called "Diff_limma".

Value

Differential expression output table for all group comparisons - outputs information for all genes, including non-significant ones.

Examples

design <- as.matrix(data.frame(Ctrl = c(rep(1, 4), rep(0,12)), TolLPS = c(rep(0, 4), rep(1, 4),
             rep(0, 8)), TollMRP8 = c(rep(0, 8), rep(1, 4), rep(0, 4)), ActLPS = c(rep(0, 12),
             rep(1, 4)), row.names = colnames(expmatrix)))
groupcomparisons=c("TolLPS-Ctrl", "TollMRP8-Ctrl", "ActLPS-Ctrl")
diff_limma_all_output <- diff_limma_all(expmatrix, design, groupcomparisons)

ShirinG/exprAnalysis documentation built on May 9, 2019, 1:28 p.m.