computeKSEA: compute kinase substrate enrichment - osama's code wrapped in...

In PNNL-CompBio/amlresistancenetworks: Calculates networks that lead to AML resistance to drugs

compute kinase substrate enrichment - osama's code wrapped in package.

Description

compute kinase substrate enrichment - osama's code wrapped in package.

Usage

computeKSEA(
  genes.with.values,
  ksea_FDR = 0.05,
  prefix = "",
  order_by = "z.score",
  height = 8.5,
  width = 11,
  NetworKIN = TRUE,
  linkedSubs = 5,
  suffix = "png"
)

Arguments

genes.with.values	data frame containing a Gene column, as well as a Residue.Both column and FC column (see KSEA app).
prot.univ	the space of all proteins we are considering

Value

KSEA output type stuff * KSEA using not only the known substrates in PSP but also the predicted substrates in NetworKIN

Author(s)

Osama

PNNL-CompBio/amlresistancenetworks documentation built on Feb. 8, 2025, 11:27 a.m.