get_snp_matrices | R Documentation |
Get SNP data matrices from VCF object(s)
get_snp_matrices(vcf_cell, vcf_donor = NULL, verbose = TRUE, donors = NULL)
vcf_cell |
a |
vcf_donor |
an optional |
verbose |
logical(1), should the function output verbose information as it runs? |
donors |
optional character vector providing a set of donors to use, by
subsetting the donors present in the |
a list containing
A
, a matrix of integers. Number of alteration reads in SNP i cell j.
D
, a matrix of integers. Number of reads depth in SNP i cell j.
R
, a matrix of integers. Number of reference reads in SNP i cell j.
GT_cells
, a matrix of integers for genotypes. The cell-SNP
configuration.
GT_donors
, a matrix of integers for genotypes. The donor-SNP
configuration.
vcf_cell <- read_vcf(system.file("extdata", "cells.donorid.vcf.gz", package = "cardelino")) vcf_donor <- read_vcf(system.file("extdata", "donors.donorid.vcf.gz", package = "cardelino")) snp_data <- get_snp_matrices(vcf_cell, vcf_donor)
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