runPSEA | R Documentation |
This is the main function to run protein set enrichment analysis for a list of proteins and their score.
runPSEA(
protein,
os.name,
blist = NULL,
pexponent = 1,
nperm = 1000,
p.adj.method = "fdr",
sig.level = 0.05,
minSize = 1
)
protein |
A dataframe with two columns. Frist column should be protein accession code, second column is the score. |
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. |
pexponent |
Enrichment weighting exponent, p. For values of p < 1, one can detect incoherent patterns in a set of protein. If one expects a small number of proteins to be coherent in a large set, then p > 1 is a good choice. |
nperm |
Number of permutation to estimate false discovery rate (FDR). Default value is 1000. |
p.adj.method |
The adjustment method to correct pvalues for multiple testing in enrichment. Run p.adjust.methods() to get a list of possible methods. |
sig.level |
The significance level to filter PTM (applies on adjusted p-value) |
minSize |
PTMs with the number of proteins below this threshold are excluded. |
Returns a list of 6: 1: A dataframe with protein set enrichment analysis (PSEA) results. Every row corresponds to a post-translational modification (PTM) keyword.
PTM: PTM keyword
pval: p-value obtained from singular enrichment analysis (SEA).
pvaladj: adjusted p-value. This column is the adjusted pvalues with p.adj.method methods calculated in SEA method.
FreqinPopulation: The frequency of PTM in UniProt.
FreqinSample: The frequency of PTM in the given list.
ES: enrichment score.
NES: enrichmnt score normalized to mean enrichment of random samples of the same size.
nMoreExtreme: number of times the permuted sample resulted in a profile with a larger ES value than abs(ES) of the sample.
size: Number of proteins in the list having this specific PTM.
Enrichment: Indicates if the proteins with the specific protein have been enriched in the list or not. NES positive is considered as enriched.
AC: Uniprot accession code (AC) of proteins with the specific PTM.
leadingEdge: the leading edge proteins are the proteins that show up in the ranked list at or before the point where the enrichment score (ES) reaches its maximum deviation from zero.
# 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)
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