writeFilesForKiwi {piano} | R Documentation

## Write files for Kiwi

### Description

Given a single object or a list of objects of class GSAres, extract the information needed for visualization in the external python function Kiwi and write it to files that can be used as input.

### Usage

    writeFilesForKiwi(gsaRes, label = "", overwrite = FALSE)

### Arguments

`gsaRes` | either an object of class `GSAres` or a list where each element is an object of class `GSAres`, as returned by the `runGSA` function.
`label` | a character string that will be appended to the names of the resulting files.
`overwrite` | a logical, whether or not to overwrite existing files with identical names.

### Details

This function takes the result from a gene set analysis as returned by the `runGSA` function and writes three files that can be directly used as input to Kiwi. Kiwi is a external function i python that can be used for network-based visualization of the GSA results (http://sysbio.se/kiwi).

### Value

Three files are written in the current directory. GSC.txt contains the gene-gene set associations, i.e. the gene set collection. GLS.txt contains the gene-level statistics. GSS.txt contains the gene set statistics.

### Author(s)

Leif Varemo piano.rpkg@gmail.com

### See Also

piano, `runGSA`, `networkPlot`

### Examples

       # Load some example GSA results:
       data(gsa_results)

       # Write the files:
       writeFilesForKiwi(gsa_results,"exp1")

[Package piano version 1.18.1 Index]