Run PTM-SEA API using a gct file as input

This function takes in a gct file (created by the read_prmsea function) and run PTM-SEA API and returns results

run_ptmsea(gct_object, lib = "iptmnet", nperm = 1000, min.overlap = 1, ...)

Arguments

lib

searched kea libraries "iptmnet" or "ptm-sea" or "all (default is "iptmnet" which uses the iptmnet mapping)
nperm

number of permutations
min.overlap

minimum overlap of target peptides with referernce peptides sets
...

additional arguments passed to the ssGSEA_ce function
gene_set

vector, HGNC gene symbols based on the differentially phosphorylated peptides

Value

list