psea2mass | R Documentation |
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.
psea2mass(x, sig.level = 0.05, number.rep = NULL)
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. |
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
# 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)
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