voomWorkflow: Function voomWorkflow

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

Description

This function runs several steps in the RNA-Seq pipeline in one fell swoop. It supports duplicateCorrelation if you provide a blocking vector. It includes low intensity filtering, filtering for protein coding genes and filters out zero effective length genes (genes shorter than library size). Then it runs TMM normalization, voomWithQualityWeights, lmFit and eBayes.

Usage

voomWorkflow(
  dgeObj,
  formula,
  projectName,
  designMatrixName,
  dupcorBlock,
  outputPath = "./",
  annotationFile,
  proteinCodingOnly = FALSE,
  sampleFraction = 0.5,
  ...
)

Arguments

dgeObj	A class dgeObj with counts, gene annotation and sample annotation
formula	A text representation of the formula you want to use (clas character not formula)
projectName	This should be the project name from Xpress or Omicsoft
designMatrixName	User defined name for the design matrix
dupcorBlock	A blocking vector to define which samples belong to the same subject to be used with the duplicateCorrelation function.
outputPath	Where to send output plots
annotationFile	Text file of key=value pairs to populate DGEobj attributes (optional but highly advised)
proteinCodingOnly	Set to TRUE to keep only protein coding genes (default = TRUE)
sampleFraction	Fraction of samples that must meet intensity thresholds to keep a gene (Default = 0.5)
...	Additional named arguments passed to the low intensity filter function to define the desired intensity filter type (see ?lowIntFilter). Settable arguments for low intensity filtering are: fracThreshold (default = 0.5), countThreshold, fpkThreshold, zfpkmThreshold, tpmThreshold. You can use countThreshold plus one other argument. If no arguments supplied here, the following defaults apply (fracThreshold=0.5, countThreshold=10, fpkThreshold=5). To disable intensity filtering use: sampleFraction = 0.

Details

To incorporate SVA analysis, you need to run SVA first and add the SVA variables to your design table. Then you can proceed with this function.

After running this step. You define your contrasts and execute runContrast to complete DGE calculations.

Value

A DGEobj with analysis results added

Author(s)

John Thompson, [e-mail]

Examples

   MyDgeObj <- voomWorkflow(MyDgeObj,
                            formula = "~ 0 + ReplicateGroup",
                            projectName = "MyProjectName",
                            designMatrixName = "ReplicateGroup",
                            annotationFile = "MyProjectName.txt",
                            proteinCodingOnly = TRUE,
                            )

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