PEIMAN2 (version 1.0.0)

plotPSEA: 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)

Value

Plot

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.

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)