LDpop: Investigates allele frequencies and linkage disequilibrium...

View source: R/LDpop.R

LDpopR Documentation

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)


timyers/ldlinkr documentation built on March 18, 2024, 2:31 a.m.