piano (version 1.12.0)

geneSetSummary: 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.

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.

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.

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")