psea2mass: Translate PSEA results for Mass Spectrometry searching tools

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

Translate PSEA results for Mass Spectrometry searching tools

Description

This function translates protein set enrihment 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

psea2mass(x, sig.level = 0.05, number.rep = NULL)

Arguments

x	A list of psea results generated by runPSEA function.
sig.level	The significance level to filter PTMs (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

# We recommend at least nperm = 1000.
# The number of permutations was reduced to 10
# to accommodate CRAN policy on examples (run time <= 5 seconds).
psea_res <- runPSEA(protein = exmplData2, os.name = 'Rattus norvegicus (Rat)', nperm = 10)
MS <- psea2mass(x = psea_res, sig.level = 0.05)

PEIMAN2 documentation built on April 11, 2025, 6:12 p.m.