ld_extract_locuszoom: Fetch linkage disequilibrium statistics for a locus of...

In mglev1n/locusplotr: Create Regional Association Plots

Fetch linkage disequilibrium statistics for a locus of interest

Description

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

## Not run: 
ld_extract_locuszoom(chrom = 16, pos = 53830055, ref = "C", alt = "G", start = 53830055 - 5e5, stop = 53830055 + 5e5, genome_build = "GRCh37", population = "ALL", metric = "rsquare")

## End(Not run)

mglev1n/locusplotr documentation built on July 31, 2024, 8:41 p.m.