Fetch linkage disequilibrium statistics for a locus of interest

This function allows the user to extract linkage disequilibrium statistics between a variant of interest and surrounding variants within a contiguous genomic region. This function uses the University of Michigan LocusZoom API (https://portaldev.sph.umich.edu/) to obtain LD information, and allows the user to specify genome-build and ancestry of interest.

Usage

ld_extract_locuszoom(
  chrom,
  pos,
  ref,
  alt,
  start,
  stop,
  genome_build = "GRCh37",
  population = "ALL",
  metric = "rsquare"
)

Arguments

chrom

Integer - chromosome of reference variant

pos

Integer - position of reference variant

ref

Character - reference allele (or effect allele) for reference variant

alt

Character - alternate allele (or non-effect allele) for reference variant

start

Integer - starting position of range of interest

stop

Integer - ending position of range of interest

genome_build

Character - Genome build - one of "GRCh37" or "GRCh38"

population

Character - 1000G genetic superpopulation - one of "ALL", "AFR", "AMR", "EAS", "EUR", "SAS"

metric

Character - one of "r", "rsquare", or "cov", referring to the correlation statistic of interest

Value

A tibble containing each variant within the supplied range surrounding the variant of interest, with the requested linkage disequilibrium information with respect to the variant of interest

Examples

if (FALSE) { # \dontrun{
ld_extract_locuszoom(chrom = 16, pos = 53830055, ref = "C", alt = "G", start = 53830055 - 5e5, stop = 53830055 + 5e5, genome_build = "GRCh37", population = "ALL", metric = "rsquare")
} # }