formatRefMat: formatRefMat

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

Description

Pre-processes the input data into a matrix of BAF values and the least/most variant SNPs within that cohort

Usage

formatRefMat(
  name,
  ref.mat,
  analysis = "baf",
  varFileName = NULL,
  saveDir = file.path(".", "CCLid"),
  bin.size = 1e+06,
  just.var = FALSE,
  fill.na = FALSE,
  snp6.dat,
  verbose = FALSE
)

Arguments

name	Name to be applied to the returned object
ref.mat	A reference matrix of all pharmacogenomic reference samples and their BAFs, typically obtained from the downloadRefCCL() function
analysis	Only 'baf' is implemented at this point
varFileName	RDS containing the variant SNP information
saveDir	Directory to save/load the variant RDS file to
bin.size	Default is set to 5e5, a variant file must be created for this bin size
just.var	Just runs the variant SNP part of the script, skips subsetting
fill.na	Fills NA with median (Default=FALSE)
snp6.dat	SNP6 probeset genomic position, accessible from CCLid::ccl_table
verbose	Verbose

Value

Returns a list object: 'ref' = matrix of SNPs by samples for least variant SNPs 'var' = list of each 'bin size' and the SNPs and their BAF that populate it

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