View source: R/runEnrichment.R
runEnrichment | R Documentation |
This function takes proteins with their UniProt accession code, runs singular enrichment (SEA) analysis, and returns enrichment results.
runEnrichment(protein, os.name, blist = NULL, p.adj.method = "BH")
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 |
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 |
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.
enrich1 <- runEnrichment(protein = exmplData1$pl1, os.name = 'Homo sapiens (Human)')
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