createContrasts: Creates contrasts for limma-voom / edgeR and DESeq2

In huzefaKhalil/dgeContrasts: Create contrasts for use with Differential Gene Expression Analysis packages such as edgeR, limma-voom and DESeq2

Description

This function automatically generates contrasts which can be used with the popular differential gene expression pipelines of limma-voom, edgeR or DESeq2.

Usage

createContrasts(
  samples,
  groups,
  contrastType = "limma",
  interactions = FALSE,
  contrastLevel = NULL
)

Arguments

samples	The samples description data frame from which the contrasts are to be constructed
groups	The column names in the samples data frame from which contrasts will be constructed
contrastType	One of limma or DESeq2
interactions	FALSE by default. If TRUE, interaction terms are also returned. Only supports two-way interactions and will throw an error if any group has more than two factor levels.
contrastLevel	An integer which can take values from 1 to the numer of groups. If it is 1, only top-level contrasts are returned. Defaults to the number of groups.

Value

A named character vector (for limma) or list (for DESeq2) with the contrasts

huzefaKhalil/dgeContrasts documentation built on Jan. 18, 2020, 7:19 p.m.