filterNoisyCurves: Viability measurements in dose-reponse curves must remain...

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Viability measurements in dose-reponse curves must remain stable or decrease monotonically reflecting response to the drug being tested. filterNoisyCurves flags dose-response curves that strongly violate these assumptions.

Description

Viability measurements in dose-reponse curves must remain stable or decrease monotonically reflecting response to the drug being tested. filterNoisyCurves flags dose-response curves that strongly violate these assumptions.

Usage

filterNoisyCurves(
  pSet,
  epsilon = 25,
  positive.cutoff.percent = 0.8,
  mean.viablity = 200,
  nthread = 1
)

Arguments

pSet	PharmacoSet a PharmacoSet object
epsilon	numeric a value indicates assumed threshold for the distance between to consecutive viability values on the drug-response curve in the analysis, out of dna, rna, rnaseq, snp, cnv
positive.cutoff.percent	numeric This value indicates that function may violate epsilon rule for how many points on drug-response curve
mean.viablity	numeric average expected viability value
nthread	numeric if multiple cores are available, how many cores should the computation be parallelized over?

Value

a list with two elements 'noisy' containing the rownames of the noisy curves, and 'ok' containing the rownames of the non-noisy curves

Examples

data(GDSCsmall)
filterNoisyCurves(GDSCsmall)

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.