substrate_fisher_test: Construct PSSM and perform Fisher Exact Test

In edpratt1/KINATESTID: A Pipeline for Kinase-Specific Artificial Peptide Design

Description

Construct PSSM and perform Fisher Exact Test

Usage

substrate_fisher_test(
  substrates_dt,
  uniprot_dt,
  type = c("aa", "aa_property"),
  property = c("property_chemical", "property_hydropathy", "property_volume",
    "property_polar", "property_charge")
)

Arguments

substrates_dt	An enzymatic preference data.table.
uniprot_dt	A data.table containing in silico negative peptide sequences for each 'uniprot_id' found in the 'substrates_dt' file.
type	Character of either 'aa' or 'aa_property' to indicate whether amino acid residues or amino acid properties should be used.
property	Character indicating which amino acid property should be analyzed. Only used if type = 'aa'. See available property options by typing 'aa_classificiation'.

Value

A list containing two data tables: 1) Exact Test P-values and 2) Fisher Exact Odds

Examples

pssm <- substrate_fisher_test(substrates_dt = uniq_subs, uniprot_dt = uniprot,
type = "aa")

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