writeFilesForKiwi: Write files for Kiwi

In piano: Platform for integrative analysis of omics data

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 [e-mail]

See Also

piano, runGSA, networkPlot

Examples

   # Load some example GSA results:
   data(gsa_results)

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

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