load_GT_vcf: Load genotype VCF into numeric values: 0, 1, or 2

In single-cell-genetics/cardelino: Clone Identification from Single Cell Data

Load genotype VCF into numeric values: 0, 1, or 2

Description

Note, the genotype VCF can be very big for whole genome. It would be more efficient to only keep the wanted variants and samples. bcftools does such jobs nicely.

Usage

load_GT_vcf(vcf_file, rowname_format = "full", na.rm = TRUE, keep_GP = TRUE)

Arguments

vcf_file	character(1), path to VCF file for donor genotypes
rowname_format	the format of rowname: NULL is the default from vcfR, short is CHROM_POS, and full is CHROM_POS_REF_ALT
na.rm	logical(1), if TRUE, remove the variants with NA values
keep_GP	logical(1), if TRUE, check if GP (genotype probability) exists it will be returned

Value

A list representing the loaded genotype information with two components: GT, the usual numeric representation of genotype and GP the genotype probabilities. Note that if keep_GP is false the GP component will be NULL.

Examples

vcf_file <- system.file("extdata", "cellSNP.cells.vcf.gz",
    package = "cardelino"
)
GT_dat <- load_GT_vcf(vcf_file, na.rm = FALSE)

single-cell-genetics/cardelino documentation built on Nov. 22, 2022, 4:05 p.m.