combineGSE {RTopper} | R Documentation

## Combines GSE results

### Description

Combines GSE results obtained from a sepatate set of gene-to-phenotypes scores

### Usage

    combineGSE(gseOut, method)

### Arguments

`gseOut` | a list of lists containing the enrichment results to be combined. This is usually the the output of `runBatchGSE` obtained from a set of distinct genes-to-phenotype scores (usually one per genomic platform)
`method` | character, this argument specifies the method used to combine the enrichment results obtained from distinct genes-to-phenotype scores (usually one per genomic platform). Available options are the computation of the geometric or arithmetic means, the use of the median, the selection of the minimun or the maximum enrichment score, and the random selection of a score (respectively `"geometricMean"`, `"mean"`, `"median"`, `"min"`, `"max"`, and `"random"`)

### Details

This function summarize enrichment results obtained from distinct gene-to-phenotypes scores (usually one per genomic platform) by one of several alternative methods.

### Value

The output is a list of lists containing integrated enrichment results for all FGS collections

### Author(s)

Luigi Marchionni marchion@jhu.edu

### References

Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, and Giovanni Parmigiani. "Integrating diverse genomic data using gene sets." Manuscript submitted.

### Examples

    ###load gse analysis results for separate gene-to-phenotype score
    data(gseResultsSep)

    ###combine enrichment score results using geometric mean
    gseABS.sep.geoMean <- combineGSE(gseResultsSep, method="geometricMean")

    ###combine enrichment score results using maximum value
    gseABS.sep.max <- combineGSE(gseResultsSep, method="max")

[Package RTopper version 1.28.0 Index]