create_contrast: Design and contrast matrices

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

Description

create_design - Function to generate design matrix for edgeR and limma+voom.

create_contrast - Function to generate contrast matrix for edgeR, limma+voom, and DESEq2 analyses.

Usage

create_design(se = NULL, block.column = NULL)

create_contrast(design = NULL)

Arguments

se	A SummarizedExperiment object containing the sample metadata information.
block.column	The column in 'samples' containing information regarding block or batch effect.
design	Design matrix produced by create_design.

Value

create_design returns a design matrix.

create_contrast returns a contrast matrix.

Examples

## Not run: 
design <- create_design(se, block.column = "replicate")
contrast <- create_contrast(design = design)

## End(Not run)

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