LDlinkR (version 1.1.2)

LDmatrix: Generates a data frame of pairwise linkage disequilibrium statistics.

Description

Generates a data frame of pairwise linkage disequilibrium statistics.

Usage

LDmatrix(snps, pop = "CEU", r2d = "r2", token = NULL, file = FALSE)

Arguments

snps

list of between 2 - 1,000 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"

r2d

r2d, either "r2" for LD R2 or "d" for LD D', default = "r2"

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 {
LDmatrix(c("rs3", "rs4", "rs148890987"),
                    "YRI", "r2",
                    token = Sys.getenv("LDLINK_TOKEN"))
                 
# }
# NOT RUN {
# }