sea2mass

This function translates singular enrichment analysis results and extracts the required information
for mass spectometry searching tools. The subset of protein modifications is from <a href="https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo">https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo</a>.

Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Uladzislau Vadadokhau, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2025) <doi:10.1002/pmic.202400238>.

Nickchi Payman

PEIMAN2

Post-Translational Modification Enrichment, Integration, and
Matching Analysis

Mohieddin Jafari

Payman Nickchi

sea2mass function

<dl><dt>x</dt>
<dd>A dataframe of single enrichment analysis results generated by <code>runEnrichment</code> function.</dd>
<dt>sig.level</dt>
<dd>The significance level to filter pathways (applies on adjusted p-value). Default value is 0.05.</dd>
<dt>number.rep</dt>
<dd>Only consider PTM terms that occurred more than a specific number of times in UniProt. This number is set
by number.rep parameter. The default value is NULL.</dd></dl>

Arguments

This function translates singular enrichment analysis results and extracts the required information
for mass spectometry searching tools. The subset of protein modifications is from <a href='https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo'>https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo</a>.

Translate SEA results for Mass Spectrometry searching tools — sea2mass

<dl>

<dt>x</dt>
<dd>A dataframe of single enrichment analysis results generated by <code>runEnrichment</code> function.</dd>


<dt>sig.level</dt>
<dd>The significance level to filter pathways (applies on adjusted p-value). Default value is 0.05.</dd>


<dt>number.rep</dt>
<dd>Only consider PTM terms that occurred more than a specific number of times in UniProt. This number is set
by number.rep parameter. The default value is NULL.</dd>

</dl>

sea2mass: Translate SEA results for Mass Spectrometry searching tools

Description

Usage

Value

Arguments

Examples