link_LD: Obtain LD at a locus from LDlink

In myles-lewis/locuszoomr: Gene Locus Plot with Gene Annotations

Obtain LD at a locus from LDlink

Description

Adds LD information to a 'locus' class object. It queries LDlink (https://ldlink.nci.nih.gov/) via the LDlinkR package to retrieve linkage disequilibrium (LD) information on a reference SNP.

Usage

link_LD(
  loc,
  pop = "CEU",
  r2d = "r2",
  token = "",
  method = c("proxy", "matrix"),
  genome_build = loc$genome,
  ...
)

Arguments

loc	Object of class 'locus' generated by locus()
pop	A 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU". Passed to LDlinkR::LDmatrix().
r2d	Either "r2" for LD r^2 or "d" for LD D', default = "r2". Passed to LDlinkR::LDmatrix() or LDproxy().
token	Personal access token for accessing 1000 Genomes LD data via LDlink API. See LDlinkR package documentation.
method	Either "proxy" or "matrix". Controls whether to use LDproxy() or LDmatrix() to obtain LD data.
genome_build	Choose between one of the three options: 'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19).
...	Optional arguments which are passed on to LDlinkR::LDmatrix() or LDlinkR::LDproxy()

Details

The argument method controls which LDlinkR function is used to retrieve LD data. LDmatrix() is slower but usually more complete for small queries (<1000 SNPs). However, it has a limit of 1000 SNPs which can be queried. LDproxy() is faster but data on some SNPs may be absent.

Note, SNPs have to be correctly formatted as required by LDlinkR, either as rsID (works with either method) or chromosome coordinate e.g. "chr7:24966446" (works with LDproxy only). Default genome build is grch37, see LDproxy() or LDmatrix().

Value

Returns a list object of class 'locus'. LD information is added as a column ld in list element data.

See Also

locus()

myles-lewis/locuszoomr documentation built on Nov. 29, 2024, 4:49 p.m.