runEnrichment {PEIMAN2} | R Documentation |
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, 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 |
p.adj.method |
The adjustment method to correct for multiple testing. The default value is 'BH'.
Run/see |
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)')