gsnDistanceHistogram

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

gsnDistanceHistogram function

<dl><dt>object</dt>
<dd>A GSNData object</dd>
<dt>distance</dt>
<dd>A distance, or even a character vector of distances, e.g. c("lf", "jaccard", "stlf").</dd>
<dt>dist.matrix</dt>
<dd>The names of distance matrices, which can be "raw" for the distance stored in "matrix",
"pared" for the distances stored in "pared", and "edges" for the distances stored in "edges". In general,
the distances in "edges" will be the same as those in "pared", but this may not always be true.</dd>
<dt>stat</dt>
<dd>Can be "percent", "count", "density", or "cumulative". This determines how the data are visualized.</dd>
<dt>colors</dt>
<dd>Currently, this does nothing, but will eventually allow the user to specify custom colors. Stay
tuned.</dd>
<dt>bins</dt>
<dd>The number of bins, for histograms ("percent" or "count").</dd></dl>

Arguments

gsnDistanceHistogram — gsnDistanceHistogram

<dl>

<dt>object</dt>
<dd>A GSNData object</dd>


<dt>distance</dt>
<dd>A distance, or even a character vector of distances, e.g. c("lf", "jaccard", "stlf").</dd>


<dt>dist.matrix</dt>
<dd>The names of distance matrices, which can be "raw" for the distance stored in "matrix",
"pared" for the distances stored in "pared", and "edges" for the distances stored in "edges". In general,
the distances in "edges" will be the same as those in "pared", but this may not always be true.</dd>


<dt>stat</dt>
<dd>Can be "percent", "count", "density", or "cumulative". This determines how the data are visualized.</dd>


<dt>colors</dt>
<dd>Currently, this does nothing, but will eventually allow the user to specify custom colors. Stay
tuned.</dd>


<dt>bins</dt>
<dd>The number of bins, for histograms ("percent" or "count").</dd>

</dl>

gsnDistanceHistogram: gsnDistanceHistogram

Description

Usage

Value

Arguments

Details

See Also