LDlinkR (version 1.1.2)

LDhap: 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)

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.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 {
LDhap(c("rs3", "rs4", "rs148890987"), "CEU", token = Sys.getenv("LDLINK_TOKEN"))
# }
# NOT RUN {
LDhap("rs148890987", c("YRI", "CEU"), token = Sys.getenv("LDLINK_TOKEN"))
# }
# NOT RUN {
# }