LDlinkR (version 1.1.2)

SNPchip: 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)

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.nci.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.

Value

a data frame

Examples

# NOT RUN {
SNPchip(c("rs3", "rs4", "rs148890987"), "ALL",
                 token = Sys.getenv("LDLINK_TOKEN"))
               
# }
# NOT RUN {
SNPchip(c("rs3", "rs4", "rs148890987"),
                 c("A_CHB2", "A_SNP5.0"),
                 token = Sys.getenv("LDLINK_TOKEN"))
                 
# }
# NOT RUN {
SNPchip("rs148890987", "ALL_Affy", token = Sys.getenv("LDLINK_TOKEN"))
# }
# NOT RUN {
# }