| psea2mass {PEIMAN2} | R Documentation |
Translate PSEA results for Mass Spectrometry searching tools
Description
This function translates protein set enrihment analysis results and extracts the required information for mass spectometry searching tools. The subset of protein modifications is from https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo.
Usage
psea2mass(x, sig.level = 0.05, number.rep = NULL)
Arguments
x |
A list of psea results generated by |
sig.level |
The significance level to filter PTMs (applies on adjusted p-value). Default value is 0.05 |
number.rep |
Only consider 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
A database of subset of protein modifications:
id: a unique identification for each subset of protein modifications, PSI-MOD.
name: the name of modification.
def: definition of PSI-MOD definition
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)
MS <- psea2mass(x = psea_res, sig.level = 0.05)