plotPSEA: Plot the results of protein set enrichment analysis (PSEA)

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

Plot the results of protein set enrichment analysis (PSEA)

Description

plotPSEA can be used to plot the results of protein set enrichment analysis (psea) for a set of proteins obtained from an experiment.

Usage

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

Arguments

x	A data frame returned by runPSEA function.
y	Default value is NULL. If provided by a protein set enrichment results, the matching results of x and y are plotted.
sig.level	The significance level applied on adjusted p-value by permutation to filter pathways for plotting. The default value is 0.05
number.rep	Only plot 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

Plot

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)
plotPSEA(psea_res, sig.level = 0.05)

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