pipeDESeq2: A pipeline for DESeq2

In jtlovell/RNAseqDE: A pipeline for differential expression analyses in R

Description

pipeDESeq2 Run a pipeline of DESeq2 (if installed) functions for differential gene expression.

Usage

pipeDESeq2(counts, info, formula = NULL, reduced = NULL,
  testType = "Wald", geneIDs = NA, verbose = TRUE, ...)

Arguments

counts	A count matrix
info	An experimental design matrix
formula	A character string that can be coerced to a formula. Specify if a contrast model is not desired.
reduced	If testType = "LRT", a character string that can be coerced to a formula that represents a sub model to formula. If multiple formulae are specified, the number of formulae must match that of the formula argument. All reduced formulae must be sub models of the respective formula. If testType = "Wald", ignored.
testType	The type of statistical test to run. Possible options are "Wald" (Default) or "LRT". The latter requires the user to specify all full (formula) and reduced models to test.
geneIDs	The names of genes. If NA, use row names from counts matrix
verbose	Logical, return progress updates?
...	additional arguments to pass to DESeq.

Details

This function runs the following pipeline:

• 1. DESeq's pipeline using the specified test

• 2. Extraction of results (from DESeq2::results)

• 3. Renaming of columns and combining results across tests

Value

a list with 2 elements (if simple=TRUE) the statsistics generated from DESeq2::results

Examples

## Not run: 
library(DESeq2)
data(kidney)
counts<-kidney$counts
counts<-counts[sample(1:nrow(counts),1000),]
info<-data.frame(rep=kidney$replic,
                 treatment=kidney$treatment)
stats<-pipeDESeq(counts=counts, info=info,
   formula = " ~ treatment")
stats<-pipeLIMMA(counts=counts, info=info,
   formula = " ~ treatment",
   reduced= "~ 1",
   testType = "LRT")

## End(Not run)

jtlovell/RNAseqDE documentation built on May 10, 2019, 8:06 a.m.