gseResultsSep: A list of separated gene set enrichment p-values to be used...

In marchionniLab/RTopper: This package is designed to perform Gene Set Analysis across multiple genomic platforms

A list of separated gene set enrichment p-values to be used to run the examples in the RTopper package

Description

A list containing distinct named numeric vectors corresponding to the gene set enrichment p-value separately computed with runBatchGSE for each distinct data set. Note that for each data set there are two set of p-values, one for GO and one for KEGG. These separate p-values can be combined across data sets by the combineGSE function. Can be used as input to adjustPvalGSE.

Usage

 data(gseResultsSep) 

Format

This object is a list of length four:

"dat.affy": a list of legnth two: "go" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 GO terms on Affymetrix gene expression data; "keg" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 KEGG pathways on Affymetrix gene expression data;

"dat.agilent": a list of legnth two: "go" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 GO terms on Agilent gene expression data; "keg" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 KEGG pathways on Agilent gene expression data;

"dat.cnvHarvard": a list of legnth two: "go" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 GO terms on Harvard CNV data; "keg" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 KEGG pathways on Harvard CNV data;

"dat.cnvMskcc": a list of legnth two: "go" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 GO terms on MSKCC CNV data; "keg" is a numeric vector of length 5, containing the p-values resulting from gene set enrichment analysis of 5 KEGG pathways on MSKCC CNV data;

Source

Computed using the runBatchGSE function from the TCGA data contained in sepScores and fgsList.

Examples

data(gseResultsSep)
class(gseResultsSep)
names(gseResultsSep)
str(gseResultsSep)

marchionniLab/RTopper documentation built on Oct. 29, 2022, 8:14 a.m.