generate_substrates: Generate and score candidate artificial peptide substrate...
In edpratt1/KINATESTID: A Pipeline for Kinase-Specific Artificial Peptide Design

Generate and score candidate artificial peptide substrate sequences

generate_substrates(
  fisher_tables,
  uniprot_dt,
  screener_dt,
  target_kinase,
  screening_kinase = "ALL",
  n_hits = NULL
)

`fisher_tables`	A list containing two data tables: 1) Exact Test P-values and 2) Fisher Exact Odds.
`uniprot_dt`	A data.table containing in silico negative peptide sequences for each 'uniprot_id' found in the 'substrates_dt' file.
`screener_dt`	A four-element list generated using the 'multi_screener()' function.
`target_kinase`	Abbreviation (typically 3 letter) for the enzyme the substrate is to be optimized for.
`screening_kinase`	A vector of kinases to optimize against. Setting screening_kinase = "ALL" will screen against every enzyme in the existing screener file.
`n_hits`	The top 'n_hits' substrates scored to be active for 'target_kinase and the lowest substrate scores for all other enzymes in the screener panel.

A four-element list containing: 1) Position-specific candidate amino acid residues, 2) Table of generated substrate scores for enzymes specified by 'screening_kinase', 3) Table of generated substrate sequences, and 4) The top 'n_hits' candidate substrates.

edpratt1/KINATESTID documentation built on Feb. 5, 2022, 1:21 p.m.