go_gene2go

note that this file lacks parent/child relations, so we only learn 'direct annotations'

Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.

Frank Koopmans

goat

Gene Set Analysis Using the Gene Set Ordinal Association Test

go_gene2go function

<dl><dt>f</dt>
<dd>full path to gene2go file stored on the computer, e.g. previously downloaded from https://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz</dd>
<dt>taxid_filter</dt>
<dd>return gene annotations only for the specified taxonomy identifier (integer value). Typical options are 9606 (Human, the default) or 10090 (mouse). Importantly, select the taxonomy/organism that is also in your input gene list (which typically contains human Entrez gene identifiers)</dd></dl>

Arguments

parse gene2go file — go_gene2go

<dl>

<dt>f</dt>
<dd>full path to gene2go file stored on the computer, e.g. previously downloaded from https://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz</dd>


<dt>taxid_filter</dt>
<dd>return gene annotations only for the specified taxonomy identifier (integer value). Typical options are 9606 (Human, the default) or 10090 (mouse). Importantly, select the taxonomy/organism that is also in your input gene list (which typically contains human Entrez gene identifiers)</dd>

</dl>

go_gene2go: parse gene2go file

Description

Usage

Value

Arguments