pipeDESeq2: A pipeline for DESeq2

Description Usage Arguments Details Value Examples

View source: R/pipeDESeq2.R

Description

pipeDESeq2 Run a pipeline of DESeq2 functions for differential gene expression.

Usage

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pipeDESeq2(counts, info, formula = NULL, reduced = NULL, testNames = NULL,
  contrasts = NULL, contrastFormula = NULL, contrastNames = NULL,
  returnNormData = "none", geneIDs = NA, verbose = TRUE,
  fitType = "parametric", quiet = TRUE, betaPrior = F,
  modelMatrixType = "standard", parallel = F, minReplicatesForReplace = 7,
  ...)

Arguments

counts

A count matrix, row names should be gene IDs

info

An experimental design matrix

formula

If specified, perform a likelihood ratio test. A vector of character strings that can be coerced into a formula. Must be of the same length as reduced. Specifies base formulas for LRT.

reduced

A character vector of the same length as formula, which can be coerced to a formula that represents a sub model to formula. All reduced formulae must be sub models of the respective formula.

testNames

A character string of names for the LRT, if specified, must be the same length as formula and reduced.

contrasts

A list of character vectors that can be input into DESeq2::results contrasts argument.

contrastFormula

The formula specifying the design matrix for the contrasts. Keep in mind that this formula specifies how the model is fit and can affect inference of the effects of contrasts.

contrastNames

Names for the contrasts. Must be the same length as contrasts

returnNormData

If NULL (default), no transformed data is returned. Other options are "rlog" and "vst" which return rlog and variance stabilized data respecitvel.

geneIDs

The names of genes. If NA, use row names from counts matrix

verbose

Logical, return progress updates?

fitType

Passed to DESeq. Default is "parametric"

quiet

Should messages from DESeq2 be suppressed?

betaPrior

Passed to DESeq. Default is F

modelMatrixType

Passed to DESeq. Default is "standard"

parallel

Passed to DESeq. Default is F

minReplicatesForReplace

Passed to DESeq. Default is 7

...

additional arguments to pass to DESeq2::results

Details

This function runs the following pipeline:

Value

a list with 3 elements (if test is not run, elements are NULL):

Examples

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## Not run: 
library(deTools)
data(counts)
data(info)
stats<-pipeDESeq2(counts=counts, info=info,
   formula = c(" ~ trt"),
   reduced = c(" ~ 1"),
   testNames = c("trt"))
stats<-pipeDESeq2(counts=counts, info=info,
   contrastFormula = " ~ trt + geno",
   contrasts = list(c("geno","HAL2","FIL2")),
   contrastNames = "HvF")

stats<-pipeDESeq2(counts=counts, info=info,)
stats<-pipeDESeq2(counts=counts, info=info,
   formula = c(" ~ trt + geno + trt:geno"," ~ trt + geno", " ~ trt + geno"),
   reduced = c(" ~ trt + geno"," ~ trt"," ~ geno"),
   testNames = c("GxE","geno","trt"),
   contrastFormula = " ~ trt + geno",
   contrasts = list(c("trt","Wet","Dry"),c("geno","HAL2","FIL2")),
   contrastNames = c("WvD","HvF"),returnNormData = "vst")

## End(Not run)

jtlovell/deTools documentation built on Sept. 27, 2017, 10 a.m.