SNPchip {LDlinkR}

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"))