exploreGSAres: Explore GSA results

In piano: Platform for integrative analysis of omics data

Description

Explore GSA results interactively in a web browser using shiny.

Usage

exploreGSAres(gsaRes, browser = TRUE, geneAnnot = NULL, genesets)

Arguments

gsaRes	an object of class GSAres, as returned from runGSA() or an object returned from runGSAhyper().
browser	a logical, whether or not to open the Shiny app in a browser window. Set to FALSE to open an interactive window directly in RStudio.
geneAnnot	a data.frame, containing gene annotation. The first column should be gene IDs matching those in gsares.
genesets	a character vector or list (named or un-named) of character vectors containing subsets of gene-set names that can be selected and displayed in the network plot.

Details

Additional gene-level information, e.g. alternative names or description, can be supplied via the geneAnnot argument. This information will show up in the gene table and the gene summary tabs.

Value

Does not return any object.

Author(s)

Leif Varemo [e-mail]

See Also

piano, runGSA, GSAheatmap, networkPlot2

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)

   # Explore results:
   ## Not run: exploreGSAres(gsares)

piano documentation built on Nov. 8, 2020, 6:27 p.m.