Get linkage disequilibrium — get_ld_in

Get LD from a group of snps or a single tag snp to all snps in a window.

Usage

get_ld_in_window(
  qtl.df = NULL,
  tag.snp = NULL,
  window,
  plink.path = NULL,
  geno.bed,
  in.dir,
  out.dir = NULL,
  verbose = TRUE
)

qtl.df: data.frame, table that includes list of snps to calculate LD to with columns (CHR, POS, LOGPVAL), corresponding to (chromosome, physical position, and -log10(p-value)). QTL are typically defined as hits grouped by LD by something like plink --clump
tag.snp: character, marker.ID of snp around which to calculate LD. In the form 'CHR-POS'
window: numeric, a physical distance to determine which snps to calculate LD for. Snps within this distance to the tag.snp or qtl.df snps will be calculated. The entire size of the region centered on the tag snp within which LD will be calculated is 2*window.
plink.path: character, optional, path to plink2 executable. Will overide option set by set_plink_path.
geno.bed: character, prefix of genotype files in plink (bed/bim/fam) format. Do not include ".bed" extension.
in.dir: character, directory where genotype files are located
out.dir: character, where to output some temporary files.
verbose: boolean, if TRUE, output some status reports

Named list with 2 items

table: table with marker.IDs (CHR-POS) and maximum LD in R2 for each snp to the snps in the qtl.df or LD to tag.snp
key.snp: marker.ID corresponding to the middle of the window, either the max(LOGPVAL) of qtl.df or tag.snp. useful to retain for downstream functions.
qtl.snps: marker.ID corresponding to the markers in the qtl.df. useful to retain for downstream functions.

When supplying a group a snps, the ld retained for a given snp is the maximum LD of the given snp to the snps in the group.

# work in progress