run_limma: Run limma+voom

In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R

Description

Function to run voom normalisation (with quality weights) followed by limma on a DGE object.

Usage

run_limma(dge = dge, design = design, contrast = contrast,
  adjust.method = "BH", p.value = 0.05)

Arguments

dge	DGE object produced by DGEList.
design	Design matrix produced by create_design.
contrast	Contrast matrix produced by create_contrast.
adjust.method	Method to be used for adjustment of nominal p-values. May be one of "BH", "bonferroni", "holm", "hochberg", "hommel", "BY".
p.value	Value between 0 and 1. Adjusted p-value for the differential expression analysis.

Value

Results of limma analysis

Examples

## Not run: 
qlf <- run_limma(dge, design, contrast.matrix)

## End(Not run)

anilchalisey/parseR documentation built on May 7, 2019, 7:45 a.m.