get_LD_vcf: Compute LD from VCF file

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

Compute LD from VCF file

Description

Imports a subset of a local or remote VCF file that matches your locus coordinates. Then uses ld to calculate LD on the fly.

Usage

get_LD_vcf(
  locus_dir = tempdir(),
  query_dat,
  LD_reference,
  query_genome = "hg19",
  target_genome = "hg19",
  superpopulation = NULL,
  samples = NULL,
  overlapping_only = TRUE,
  leadSNP_LD_block = FALSE,
  force_new = FALSE,
  force_new_maf = FALSE,
  fillNA = 0,
  stats = "R",
  as_sparse = TRUE,
  subset_common = TRUE,
  remove_tmps = TRUE,
  nThread = 1,
  conda_env = "echoR_mini",
  verbose = TRUE
)

Arguments

locus_dir	Storage directory to use.
query_dat	SNP-level summary statistics subset to query the LD panel with.
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.
query_genome	Genome build of the query_dat.
target_genome	Genome build of the LD panel. This is automatically assigned to the correct genome build for each LD panel except when the user supplies custom vcf/LD files.
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.
overlapping_only	Remove variants that do not overlap with the positions in query_dat.
leadSNP_LD_block	Only return SNPs within the same LD block as the lead SNP (the SNP with the smallest p-value).
force_new	Force the creation of a new VCF subset file even if one exists.
force_new_maf	Download UKB_MAF file again.
fillNA	When pairwise LD between two SNPs is NA, replace with 0.
stats	LD stats to r
as_sparse	Convert the LD matrix to a sparse matrix.
subset_common	Subset LD_matrix and dat to only the SNPs that are common to them both.
remove_tmps	Remove all intermediate files like vcf, npz, and plink files.
nThread	Number of threads to parallelize over.
conda_env	Conda environments to search in. If NULL (default), will search all conda environments.
verbose	Print messages.

See Also

Other LD: check_population_1kg(), compute_LD(), filter_LD(), get_LD(), get_LD_1KG(), get_LD_1KG_download_vcf(), get_LD_UKB(), get_LD_matrix(), get_locus_vcf_folder(), ldlinkr_ldproxy_batch(), plot_LD(), popDat_1KGphase1, popDat_1KGphase3, rds_to_npz(), saveSparse(), save_LD_matrix(), snpstats_get_MAF()

Examples

 
query_dat <-  echodata::BST1[seq(1, 50), ]
locus_dir <- echodata::locus_dir
locus_dir <- file.path(tempdir(), locus_dir) 
LD_reference <- system.file("extdata", "BST1.1KGphase3.vcf.bgz",
    package = "echodata"
)
LD_list <- get_LD_vcf(
    locus_dir = locus_dir,
    query_dat = query_dat,
    LD_reference = LD_reference) 

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.