geneSetSummary: Gene set summary

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

View source: R/geneSetSummary.R

Description

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

Usage

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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 [email protected] and Intawat Nookaew [email protected]

See Also

piano, runGSA, GSAsummaryTable

Examples

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   # 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")

piano documentation built on Nov. 1, 2018, 2:23 a.m.