compareVcf: compareVcf

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

Description

Checks a VCF file(s) against reference dataset to look for similarity to any known cell lines

Usage

compareVcf(
  vcfFile,
  var.dat,
  ref.mat,
  max.snps = 1e+06,
  ids = NULL,
  sampletype = "RNA",
  snp6.dat,
  ...
)

Arguments

vcfFile	Path to VCF file to check against reference datasets
var.dat	Variance data (list)
ref.mat	Reference matrix (matrix)
max.snps	Max number of SNPs to reduce
ids	IDs
sampletype	Strictly for labelling purposes
snp6.dat	SNP6 probeset genomic position, accessible from CCLid::ccl_table
...	Extra param

Value

Matrix: Containing reference matrix subsetted to common SNPs as the input VCF, as well as a left-joined VCF data

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