geneSetSummary: Gene set summary

In varemo/piano: Platform for integrative analysis of omics data

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 [e-mail] and Intawat Nookaew [e-mail]

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")

varemo/piano documentation built on Sept. 19, 2022, 12:01 p.m.