LDhap: Calculates population specific haplotype frequencies of all...

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

Calculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.

Description

Calculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.

Usage

LDhap(
  snps,
  pop = "CEU",
  token = NULL,
  file = FALSE,
  table_type = "haplotype",
  genome_build = "grch37",
  api_root = "https://ldlink.nih.gov/LDlinkRest"
)

Arguments

snps	list of between 1 - 30 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446")
pop	a 1000 Genomes Project population, (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
file	Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE.
table_type	Choose from one of four options available to determine output format type...'haplotype', 'variant', 'both' and 'merged'. Default = "haplotype".
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 or list

Examples

## Not run: LDhap(c("rs3", "rs4", "rs148890987"), "CEU", token = Sys.getenv("LDLINK_TOKEN"))
## Not run: LDhap("rs148890987", c("YRI", "CEU"), token = Sys.getenv("LDLINK_TOKEN"))

CBIIT/LDlinkR documentation built on April 15, 2024, 3:18 p.m.