LDlinkR (version 1.4.0)

LDpop: Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.

Description

Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.

Usage

LDpop(
  var1,
  var2,
  pop = "CEU",
  r2d = "r2",
  token = NULL,
  file = FALSE,
  genome_build = "grch37",
  api_root = "https://ldlink.nih.gov/LDlinkRest"
)

Value

a data frame

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"

r2d

either "r2" for LD R2 or "d" for LD D', default = "r2"

token

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

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) LDpop(var1 = "rs3", var2 = "rs4",
               pop = "YRI", r2d = "r2",
               token = Sys.getenv("LDLINK_TOKEN"))