runGSEA: Apply GSEA to a voom normalized data set for a specific model...

In carlmurie/RNASeqUtilities: Helper functions for RNASeq analysis and presentation

Description

Apply GSEA to a voom normalized data set for a specific model and coefficients.

Usage

runGSEA(voomDat, geneIndices, coefs, labels = NULL, onlySigs = FALSE,
  FDRCut = 0.2)

Arguments

voomDat	Eset of voom normalised data which must include the design. This is the output of voom function in limma.
geneIndices	List of gene indices corresponding to gene sets. It is created by ids2indices function in limma.
coefs	Vector of coefficients to test. They must map to a coefficient in the design matrix in 'voomDat'.
labels	Vector of character strings that labels each coefficient being tested. This allows for more human readable labels than the lmFit coefficients. Labels must map one to one to 'coefs'.
onlySigs	Boolean: if TRUE return only genesets that pass the 'FDRCut' threshold (return -1 if no significant gene sets) else return all genesets. Default is FALSE.
FDRCut	FDR threshold to use to determine significance. Default is 0.2.

Value

List of camera results. Each element is the result for a single coefficient from 'coefs'

carlmurie/RNASeqUtilities documentation built on Sept. 1, 2019, 11:54 p.m.