driftOverlapMetric: driftOverlapMetric

In quevedor2/CCLid: Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets

Description

Calculate the amount of overlap between the CN and BAF inferred drift GRanges objects

Usage

driftOverlapMetric(
  gr.baf,
  gr.cn,
  cell.ids,
  ov.frac = seq(0, 1, by = 0.01),
  baf.z = 4,
  cn.z = 2,
  cn.gtruth = FALSE
)

Arguments

gr.baf	GRangesList of cell lines an their BAF-drifted regions
gr.cn	GRangesList of cell lines an their CN-drifted regions
cell.ids	Vector of cell line names to check drift of
ov.frac	overlap fraction cutoff: (Default: seq(0, 1, by=0.01))
baf.z	z threshold for BAF difference
cn.z	z threshold for L2R difference
cn.gtruth	if TRUE, isolates BAF for only CN drifted regions

Value

List containing the following elements: "model" = non-linear least-square model fitted to concordance and sensitvity "saturation"=Matrix of total saturation and concordance cutoff "sens"=Matrix of sensitivity value for each concordance cutoff "dat"=Matrix of concordance cutoff by cell lines

quevedor2/CCLid documentation built on July 15, 2020, 4:05 a.m.