LDlinkR (version 1.4.0)

LDpair: Investigates potentially correlated alleles for a pair of variants.

Description

Investigates potentially correlated alleles for a pair of variants.

Usage

LDpair(
  var1,
  var2,
  pop = "CEU",
  token = NULL,
  output = "table",
  file = FALSE,
  genome_build = "grch37",
  api_root = "https://ldlink.nih.gov/LDlinkRest"
)

Value

text or data frame, depending on the output option

Arguments

var1

the first RS number or genomic coordinate (e.g. "chr7:24966446")

var2

the second RS number or genomic coordinate (e.g. "ch7:24966446")

pop

a 1000 Genomes Project population(s), (e.g. YRI or CEU), multiple allowed, default = "CEU"

token

LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess

output

two output options available, "text", which displays a two-by-two matrix displaying haplotype counts and allele frequencies along with other statistics, or "table", which displays the same data in rows and columns, default = "table"

file

Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE.

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).

api_root

Optional alternative root url for API.

Examples

if (FALSE) LDpair(var1 = "rs3", var2 = "rs4", pop = "YRI", token = Sys.getenv("LDLINK_TOKEN"))
if (FALSE) LDpair("rs3", "rs4", "YRI", token = Sys.getenv("LDLINK_TOKEN"), "text")