GSAsummaryTable: Gene set analysis summary table

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

Gene set analysis summary table

Description

Displays or saves a summary table of the results from runGSA.

Usage

GSAsummaryTable(gsaRes, save = FALSE, file = NULL)

Arguments

gsaRes	an object of class GSAres, as returned from runGSA().
save	a logical, whether or not to save the table.
file	a character string giving the file name to save to.

Details

The table is by default saved as an .xls file, if file is unused.

Value

The summary table as a data.frame (returned invisibly if save=TRUE).

Author(s)

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

See Also

piano, runGSA, networkPlot, GSAheatmap

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)
      
   # Summary table:
   GSAsummaryTable(gsares)  

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