combineGSE: Combines GSE results

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

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 [e-mail]

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")

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