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

View source: R/read_data.R

load_GT_vcfR Documentation

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)

davismcc/cardelino documentation built on Nov. 19, 2022, 2:44 a.m.