runEnrichment: Run singular enrichment analysis (SEA) for a given list of...

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

Run singular enrichment analysis (SEA) for a given list of protein

Description

This function takes proteins with their UniProt accession code, runs singular enrichment (SEA) analysis, and returns enrichment results.

Usage

runEnrichment(protein, os.name, blist = NULL, p.adj.method = "BH")

Arguments

protein	A character vector with protein UniProt accession codes.
os.name	A character vector of length one with exact taxonomy name of species. If you do not know the the exact taxonomy name of species you are working with, please read getTaxonomyName.
blist	The background list will be substituted with the complete set of UniProt reviewed proteins to facilitate the analysis with a background list. The default value is NULL. Alternatively, if a vector of UniProt Accession Codes is provided, it will serve as the background list for the enrichment analysis.
p.adj.method	The adjustment method to correct for multiple testing. The default value is 'BH'. Run/see p.adjust.methods to get a list of possible methods.

Value

The result is a dataframe with the following columns:

• PTM: Post-translational modification (PTM) keyword

• FreqinUniprot: The total number of proteins in UniProt with this PTM.

• FreqinList: The total number of proteins in the given list with this PTM.

• Sample: Number of proteins in the given list.

• Population: Total number of proteins in the current version of PEIMAN database with this PTM.

• pvalue: The p-value obtained from hypergeometric test (enrichment analysis).

• corrected pvalue: Adjusted p-value to correct for multiple testing.

• AC: Uniprot accession code (AC) of proteins with each PTM.

Examples

enrich1 <- runEnrichment(protein = exmplData1$pl1, os.name = 'Homo sapiens (Human)')

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