runContrasts: Function runContrasts

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Take a DGEObj and a named list of contrasts to build. The DGEobj must contain a limma Fit object and associated DesignMatrix. Returns the DGEobj with contrast fit(s), contrast matrix and topTable/topTreat dataframes added.

Usage

runContrasts(
  dgeObj,
  designMatrixName,
  contrastList,
  contrastSetName = fitName,
  runTopTable = TRUE,
  runTopTreat = FALSE,
  FoldChangeThreshold = 1.5,
  PvalueThreshold = 0.01,
  FDRthreshold = 0.1,
  runEBayes = TRUE,
  robust = TRUE,
  proportion = 0.01,
  Qvalue = FALSE,
  IHW = FALSE,
  verbose = FALSE
)

Arguments

dgeObj	A DGEobj object containing a Fit object and design matrix (required)
designMatrixName	The name of the design matrix within dgeObj to use for contrast analysis (required)
contrastList	A named list of contrasts (required)
contrastSetName	Name for the set of contrasts specified in contrastList. Defaults to "fitName_cf". Change only if you need to create 2 or more contrast sets from the same fit.
runTopTable	runs topTable on the specified contrasts (Default = TRUE)
runTopTreat	runs topTreat on the specified contrasts (Default = FALSE)
FoldChangeThreshold	Only applies to TopTreat (Default = 1.5)
PvalueThreshold	Default = 0.01
FDRthreshold	Default = 0.1
runEBayes	Runs eBayes after contrast.fit (default = TRUE)
robust	eBayes robust option (default = TRUE)
proportion	Proportion of genes expected to be differentially expressed (used by eBayes) (Default = 0.01)
Qvalue	Set TRUE to include Qvalues in topTable output (Default=FALSE)
IHW	Set TRUE to add FDR values from the IHW package (Defulat=FALSE)
verbose	Set TRUE to print some information during processing (Default=FALSE)

Details

The contrastList is a named list composed of column names from the DesignMatrix of the DGEobj. Each contrast is named to give it a short recognizable name.

Example contrastList

contrastList = list(
T1 = "treatment1 - control",
T2 = "treatment2 - control"
)

where treatment1, treatment2 and control are columns in the DesignMatrix

The returned ContrastAnalysis list contains the following objects:

• "ContrastMatrix" a matrix

• "Fit.Contrasts" a Fit object

• "TopTableList" a List of dataframes

• "TopTreatList" a List of dataframes

Value

The DGEobj with contrast fits and topTable/topTreat dataframes added.

Author(s)

John Thompson, [e-mail]

Examples

#run defaults
myDgeObj  = runContrasts (myDgeObj, myFitName, ConstrastList)
myDgeObj  = runContrasts (myDgeObj, myFitName, ConstrastList, runTopTable = TRUE
       runTopTreat=TRUE, FoldChangeThreshold = 1.25)

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.