write_gmt

Takes a gene set collection (as a named list of vectors of genes), and a filename, and writes GMT format.
Right now, keeping this private.

Create networks of gene sets, infer clusters of functionally-related gene sets based
on similarity statistics, and visualize the results. This package simplifies and accelerates
interpretation of pathways analysis data sets. It is designed to work in tandem with standard
pathways analysis methods, such as the 'GSEA' program (Gene Set Enrichment Analysis), CERNO
(Coincident Extreme Ranks in Numerical Observations, implemented in the 'tmod' package) and others.
Inputs to 'GSNA' are the outputs of pathways analysis methods: a list of gene sets (or "modules"),
pathways or GO-terms with associated p-values. Since pathways analysis methods may be used to
analyze many different types of data including transcriptomic, epigenetic, and high-throughput
screen data sets, the 'GSNA' pipeline is applicable to these data as well. The use of 'GSNA' has
been described in the following papers:
Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, et al. (2021) <doi:10.1016/j.immuni.2021.08.007>,
Collins DR, Hitschfel J, Urbach JM, Mylvaganam GH, Ly NL, Arshad U, et al. (2023) <doi:10.1126/sciimmunol.ade5872>.

Jonathan M Urbach

GSNA

Gene Set Networking Analysis Package

write_gmt function

<dl><dt>gsc</dt>
<dd>A GSC (gene set collection) as a named list of character vectors of gene symbols, where
the names of the list items correspond to gene set identifiers.</dd>
<dt>filename</dt>
<dd>An output file name.</dd></dl>

Arguments

write_gmt — write_gmt

<dl>

<dt>gsc</dt>
<dd>A GSC (gene set collection) as a named list of character vectors of gene symbols, where
the names of the list items correspond to gene set identifiers.</dd>


<dt>filename</dt>
<dd>An output file name.</dd>

</dl>

write_gmt: write_gmt

Description

Usage

Value

Arguments

Details

Examples