nzLog10

Utility function to safely (non-zero) log10 transform p-values that are bounded at
0, and may be zero or may be rounded to zero in certain contexts. To get around this, prior to
applying a log10 transformation the function adds a very small pseudocount to all the values if
any are detected to be zero. This avoids the generation of negative infinities. (See details, below.)

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

nzLog10 function

<dl><dt>x</dt>
<dd>A numerical vector containing non-negative values.</dd>
<dt>quiet</dt>
<dd>A boolean that tells the script to suppress warning messages. (default: FALSE. This
does not suppress errors, however.)</dd>
<dt>pseudocount_frxn</dt>
<dd>A numerical value that sets the added pseudocount as a fraction of the
minimum non-zero value. (default: 0.5)</dd></dl>

Arguments

nzLog10 — nzLog10

<dl>

<dt>x</dt>
<dd>A numerical vector containing non-negative values.</dd>


<dt>quiet</dt>
<dd>A boolean that tells the script to suppress warning messages. (default: FALSE. This
does not suppress errors, however.)</dd>


<dt>pseudocount_frxn</dt>
<dd>A numerical value that sets the added pseudocount as a fraction of the
minimum non-zero value. (default: 0.5)</dd>

</dl>

nzLog10: nzLog10

Description

Usage

Value

Arguments

Details

Examples