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

Description Usage Arguments Value Examples

View source: R/LDmatrix.R

Description

Generates a data frame of pairwise linkage disequilibrium statistics.

Usage

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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

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## Not run: LDmatrix(c("rs3", "rs4", "rs148890987"),
                    "YRI", "r2",
                    token = Sys.getenv("LDLINK_TOKEN"))
                 
## End(Not run)

LDlinkR documentation built on Feb. 20, 2021, 1:06 a.m.