geneSetSummary {piano} | R Documentation

## Gene set summary

### Description

Returns a summary of the statistics and gene members of a given gene set in a `GSAres` object.

### Usage

    geneSetSummary(gsaRes, geneSet)

### Arguments

`gsaRes` | an object of class `GSAres`, as returned from `runGSA()`.
`geneSet` | a character string giving the name of a gene-set.

### Details

This function can be used to access information on specific gene sets of interest. The same results are available for all gene sets using `GSAsummaryTable`.

### Value

A list with the elements `name`, containing the gene-set name, `geneLevelStats`, containing the gene-level statistics of the member genes, `directions`, containing the directions of the member genes, and `stats`, a table of the gene set statistics and p-values.

### Author(s)

Leif Varemo varemo@chalmers.se and Intawat Nookaew intawat@chalmers.se

### See Also

piano, `runGSA`, `GSAsummaryTable`

### Examples

       # Load example input data to GSA:
       data("gsa_input")

       # Load gene set collection:
       gsc <- loadGSC(gsa_input$gsc)

       # Run gene set analysis:
       gsares <- runGSA(geneLevelStats=gsa_input$pvals , directions=gsa_input$directions,
                        gsc=gsc, nPerm=500)

       # Get info on a specific gene set:
       geneSetSummary(gsares,"s1")

[Package piano version 1.20.1 Index]