get_LD_1KG_download_vcf: Download VCF subset from 1000 Genomes
In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

get_LD_1KG_download_vcf

R Documentation

Download VCF subset from 1000 Genomes

Description

Query the 1000 Genomes Project for a subset of their individual-level VCF files.

Usage

get_LD_1KG_download_vcf(
  query_granges,
  query_genome = "hg19",
  LD_reference = "1KGphase1",
  superpopulation = NULL,
  samples = character(0),
  local_storage = NULL,
  locus_dir = tempdir(),
  save_path = echotabix::construct_vcf_path(locus_dir = locus_dir, subdir = "LD",
    target_path = LD_reference, query_granges = query_granges),
  query_save = TRUE,
  force_new = FALSE,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

`query_granges`	GRanges object to be used for querying the `target_path` file. Alternatively, can be variant-level summary statistics to be converted into a GRanges object by construct_query.
`query_genome`	Genome build of the `query_dat`.
`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`.
`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.
`local_storage`	Storage folder for previously downloaded LD files. If `LD_reference` is "1KGphase1" or "1KGphase3", `local_storage` is where VCF files are stored. If `LD_reference` is "UKB", `local_storage` is where LD compressed numpy array (npz) files are stored. Set to `NULL` to download VCFs/LD npz from remote storage system.
`locus_dir`	Storage directory to use.
`save_path`	Path to save LD subset to.
`query_save`	Whether to save the queried data subset.
`conda_env`	Conda environments to search in. If `NULL` (default), will search all conda environments.
`nThread`	Number of threads to parallelize over.
`verbose`	Print messages.

Source

query_dat <- echodata::BST1 locus_dir <- file.path(tempdir(), echodata::locus_dir) query_granges <- echotabix::construct_query(query_dat=query_dat) vcf_subset.popDat <- echoLD:::get_LD_1KG_download_vcf( query_granges = query_granges, LD_reference = "1KGphase1", locus_dir = locus_dir)

Other LD: check_population_1kg(), compute_LD(), filter_LD(), get_LD(), get_LD_1KG(), get_LD_UKB(), get_LD_matrix(), get_LD_vcf(), get_locus_vcf_folder(), ldlinkr_ldproxy_batch(), plot_LD(), popDat_1KGphase1, popDat_1KGphase3, rds_to_npz(), saveSparse(), save_LD_matrix(), snpstats_get_MAF()