geneSetSummary: Gene set summary
In piano: Platform for integrative analysis of omics data

Description Usage Arguments Details Value Author(s) See Also Examples

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

1	geneSetSummary(gsaRes, geneSet)

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

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.

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.

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

piano, runGSA, GSAsummaryTable

   # 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")