LDpop: Investigates allele frequencies and linkage disequilibrium...

In LDlinkR: Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest

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"
)

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.

Value

a data frame

Examples

## Not run: LDpop(var1 = "rs3", var2 = "rs4",
               pop = "YRI", r2d = "r2",
               token = Sys.getenv("LDLINK_TOKEN"))
             
## End(Not run)

LDlinkR documentation built on May 29, 2024, 4:32 a.m.