load.data: This function loads a series of data tables or VCFs into a...

In Wedge-Oxford/dpclust: DPClust - An R package for subclonal reconstruction of tumours using sequencing data

This function loads a series of data tables or VCFs into a dataset object which is in essense a list of tables, one for each type of information

Description

This function loads a series of data tables or VCFs into a dataset object which is in essense a list of tables, one for each type of information

Usage

load.data(list_of_data_files, cellularity, Chromosome, position, WT.count,
  mut.count, subclonal.CN, no.chrs.bearing.mut, mutation.copy.number,
  subclonal.fraction, phase = NULL, is.male = T, is.vcf = F,
  ref.genome.version = "hg19", supported_chroms = c(1:22))

Arguments

list_of_data_files	A list of data file names to be read in
cellularity	A vector containing the cellularity estimates for each sample
Chromosome	String that contains the name of the column with chromosome denomination for each mutation
position	String that contains the name of the column with position denomination for each mutation
WT.count	String the colname of the column in the data files that contains the number of wild type reads
mut.count	String, the colname of the column in the data files that contains the number of mutant reads
subclonal.CN	String, the name of the total copynumber column
no.chrs.bearing.mut	String, the column that contains the number of chromosomes not bearing any mutations
mutation.copy.number	String, colname with mutation copy number estimates
subclonal.fraction	String, colname of the column that contains the subclonal fraction (or CCF) estimate for each mutation
phase	String, colname of the copy number to mutation phasing info column
is.male	Optional boolean that represents the sex, set to TRUE if male, FALSE if female. This information is used to decide whether to include X chromosome mutations
is.vcf	Optional boolean parameter whether the files to be read in are in VCF format
ref.genome.version	Optional string that represents the reference genome, required when reading in VCF files

Value

A list of tables, one for each type of information

Author(s)

sd11

Wedge-Oxford/dpclust documentation built on July 6, 2024, 2:02 p.m.