SNPchip: Find commercial genotyping chip arrays for variants of...

In timyers/ldlinkr: Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest

Find commercial genotyping chip arrays for variants of interest.

Description

Find commercial genotyping chip arrays for variants of interest.

Usage

SNPchip(
  snps,
  chip = "ALL",
  token = NULL,
  file = FALSE,
  genome_build = "grch37",
  api_root = "https://ldlink.nih.gov/LDlinkRest"
)

Arguments

snps	between 1 - 5,000 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446")
chip	chip or arrays, platform code(s) for a SNP chip array, ALL_Illumina, ALL_Affy or ALL, default=ALL
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: SNPchip(c("rs3", "rs4", "rs148890987"), "ALL",
                 token = Sys.getenv("LDLINK_TOKEN"))
               
## End(Not run)
## Not run: SNPchip(c("rs3", "rs4", "rs148890987"),
                 c("A_CHB2", "A_SNP5.0"),
                 token = Sys.getenv("LDLINK_TOKEN"))
                 
## End(Not run)
## Not run: SNPchip("rs148890987", "ALL_Affy", token = Sys.getenv("LDLINK_TOKEN"))

timyers/ldlinkr documentation built on April 17, 2024, 9:57 p.m.