getVcfDrifts: getVcfDrifts

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

Description

Check the drift of a given VCF file and all matching cell line names based on the meta-data matched IDs

Usage

getVcfDrifts(
  vcfFile,
  ref.dat,
  meta.df,
  min.depth = 5,
  centering = "extreme",
  dataset = "GDSC",
  snp6.dat
)

Arguments

vcfFile	path to vcf file
ref.dat	Refrence data containing Reference matrix and variance
meta.df	Meta file linking RNA files to cell names
min.depth	Minimum depth to consider for SNPs
centering	Centering of data method to be passed into bafDrift() function
dataset	Either 'CCLE', 'GDSC', ro 'GNE'
snp6.dat	SNP6 probeset genomic position, accessible from CCLid::ccl_table

Value

A list containing the fraction of genome drifted, as well the significantly drifted regions CNAo

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