gsc2tmod

Function to convert a GSC in the form of a named list of vectors containing gene symbols
to a object of class <code>tmod</code> which was used by the tmod prior to version <code>0.50.11</code>. This is
a wrapper for <code>makeTmod()</code> from the <code>tmod</code> package.

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

gsc2tmod function

<dl><dt>MODULES2GENES</dt>
<dd>A named list of character vectors in which the vectors correspond to gene sets
and contain gene symbols (or other gene identifiers) and the names are the corresponding gene set
identifiers.</dd>
<dt>MODULES</dt>
<dd>(optional) A data.frame containing an <code>ID</code> and a <code>Title</code> field
in the same order as the gene sets in <code>MODULES2GENES</code>. Furthermore, the row names should
(apparently) correspond to the IDs in the corresponding rows. If not provided, this will be generated
automatically.</dd>
<dt>GENES</dt>
<dd>(optional) A data frame with gene metadata. Must contain an ID column. If not provided,
this will be generated automatically.</dd></dl>

Arguments

gsc2tmod — gsc2tmod

<dl>

<dt>MODULES2GENES</dt>
<dd>A named list of character vectors in which the vectors correspond to gene sets
and contain gene symbols (or other gene identifiers) and the names are the corresponding gene set
identifiers.</dd>


<dt>MODULES</dt>
<dd>(optional) A data.frame containing an <code>ID</code> and a <code>Title</code> field
in the same order as the gene sets in <code>MODULES2GENES</code>. Furthermore, the row names should
(apparently) correspond to the IDs in the corresponding rows. If not provided, this will be generated
automatically.</dd>


<dt>GENES</dt>
<dd>(optional) A data frame with gene metadata. Must contain an ID column. If not provided,
this will be generated automatically.</dd>

</dl>

gsc2tmod: gsc2tmod

Description

Usage

Value

Arguments

See Also