run_ptmsea: Run PTM-SEA API using a gct file as input

In kalganem/creedenzymatic: creedenzymatic

Run PTM-SEA API using a gct file as input

Description

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

Usage

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

kalganem/creedenzymatic documentation built on March 31, 2024, 11:58 a.m.