computeRewiring: Score wt and mt sequences for a pwm

In omarwagih/rmimp: Predicting the impact of mutations on kinase-substrate phosphorylation

Description

Score wt and mt sequences for a pwm

Usage

computeRewiring(obj, mut_ps, prob.thresh = 0.5, log2.thresh = 1,
  include.cent = F, degenerate.pwms = F, .degenerate.groups = c("DE",
  "KR", "ILMV"))

Arguments

obj	MIMP kinase object containing PWM, auc, GMM parameters, family name, etc.
mut_ps	psnvs data frame containing wt and mt sequences computed from pSNVs function
prob.thresh	Probability threshold of gains and losses. This value should be between 0.5 and 1.
log2.thresh	Threshold for the absolute value of log ratio between wild type and mutant scores. Anything less than this value is discarded (default: 1).
include.cent	If TRUE, gains and losses caused by mutation in the central STY residue are kept

omarwagih/rmimp documentation built on May 18, 2020, 3:11 p.m.