extract_variants: Targeted extraction of variants from .vcf files using Tabix...

In vincent10kd/polygenic: Efficient and User-friendly P+T Polygenic Risk Score Creation with Summary Statistics

Targeted extraction of variants from .vcf files using Tabix files

Description

Performs targeted extraction of variants from chromosome .vcf files using Tabix index (.tbi) files.

Usage

extract_variants(
  chr_files,
  gwas_info,
  autosomes = TRUE,
  range = 0,
  grch37 = TRUE,
  keep_all = FALSE
)

Arguments

chr_files	Filenames (in order) for the chromosome-wise .vcf files
gwas_info	An object generated by get_trait_variants() or get_pQTLs(). Alternatively, a character vector of rsids.
autosomes	If TRUE, only extracts variants from the autosomes.
range	Variants are extracted from the start position until start position + range (in bp).
grch37	If TRUE, the build is grch37; if FALSE, grch38 is used.
keep_all	If TRUE, keeps all variants in the search range, even those not in gwas_info.

Value

A list with two data.frames: 'gt', containing the genotype data in number of risk alleles (0/1/2), and 'fix', containing information on the variants: rsid, chromosome, position, reference and alternative allele, and imputation quality information (e.g. DR2).

Examples

TG_gwas_info <- get_trait_variants('thrombin generation',trait_list=NULL,ask_about_efo=FALSE)
# TG_variants <- extract_variants(chromosome_files, TG_gwas_info)

vincent10kd/polygenic documentation built on Feb. 25, 2024, 10:17 a.m.