LDlinkR (version 1.1.2)

LDpop: Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.

Description

Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.

Usage

LDpop(var1, var2, pop = "CEU", r2d = "r2", token = NULL, file = FALSE)

Arguments

var1

the first RS number or genomic coordinate (e.g. "chr7:24966446")

var2

the second RS number or genomic coordinate (e.g. "ch7:24966446")

pop

a 1000 Genomes Project population(s), (e.g. YRI or CEU), multiple allowed, default = "CEU"

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 {
LDpop(var1 = "rs3", var2 = "rs4",
               pop = "YRI", r2d = "r2",
               token = Sys.getenv("LDLINK_TOKEN"))
             
# }
# NOT RUN {
# }