sea2mass: Translate SEA results for Mass Spectrometry searching tools

In PEIMAN2: Post-Translational Modification Enrichment, Integration, and Matching Analysis

Translate SEA results for Mass Spectrometry searching tools

Description

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

Usage

sea2mass(x, sig.level = 0.05, number.rep = NULL)

Arguments

x	A dataframe of single enrichment analysis results generated by runEnrichment function.
sig.level	The significance level to filter pathways (applies on adjusted p-value). Default value is 0.05.
number.rep	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.

Value

A database of subset of protein modifications:

• id: a unique identification for each subset of protein modifications, PSI-MOD.

• name: the name of modification.

• def: definition of PSI-MOD definition

Examples

enrich1 <- runEnrichment(protein = exmplData1$pl1, os.name = 'Homo sapiens (Human)')
MS      <- sea2mass(x = enrich1, sig.level = 0.05)

PEIMAN2 documentation built on June 8, 2025, 1:03 p.m.