filterNoisyCurves {PharmacoGx}R Documentation

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)


[Package PharmacoGx version 1.14.0 Index]