pipeDESeq2: A pipeline for DESeq2
In jtlovell/deTools: Some Tools to Make Differential Expression Analysis Easier

Description Usage Arguments Details Value Examples

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

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,
  ...)

`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

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

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

1. "LRT_results": The results from the likelihood ratio tests
2. "CONT_results": The results from the contrasts
3. "normData": normalized data

## 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)