exploreGSAres {piano} | R Documentation

## Explore GSA results

### 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 piano.rpkg@gmail.com

### 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)

[Package piano version 2.2.0 Index]