gseResultsSep {RTopper} | R Documentation

## 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)

[Package RTopper version 1.32.0 Index]