select_vcf_samples: Subset VCF samples
In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

select_vcf_samples

R Documentation

Subset VCF samples

Subsrt VCF samples by superpopulation.

select_vcf_samples(
  superpopulation = NULL,
  samples = NULL,
  LD_reference = "1KGphase1",
  verbose = TRUE
)

`superpopulation`	Superpopulation to subset LD panel by (used only if `LD_reference` is "1KGphase1" or "1KGphase3"). See popDat_1KGphase1 and popDat_1KGphase3 for full tables of their respective samples.
`samples`	[Optional] Sample names to subset the VCF by. If this option is used, the GRanges object will be converted to a ScanVcfParam for usage by readVcf.
`LD_reference`	LD reference to use: "1KGphase1" : 1000 Genomes Project Phase 1 (genome build: hg19). "1KGphase3" : 1000 Genomes Project Phase 3 (genome build: hg19). "UKB" : Pre-computed LD from a British European-decent subset of UK Biobank. Genome build : hg19 "<vcf_path>" : User-supplied path to a custom VCF file to compute LD matrix from. Accepted formats: .vcf / .vcf.gz / .vcf.bgz Genome build : defined by user with `target_genome`. "<matrix_path>" : User-supplied path to a pre-computed LD matrix Accepted formats: .rds / .rda / .csv / .tsv / .txt Genome build : defined by user with `target_genome`.
`verbose`	Print messages.