LDproxy_batch: Query LDproxy using a list of query variants, one per line.

Description Usage Arguments Value Examples

View source: R/LDproxy_batch.R

Description

Query LDproxy using a list of query variants, one per line.

Usage

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LDproxy_batch(snp, pop = "CEU", r2d = "r2", token = NULL, append = FALSE)

Arguments

snp

a character string or data frame listing rsID's or chromosome coordinates (e.g. "chr7:24966446"), one per line

pop

a 1000 Genomes Project population, (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

append

logical. If TRUE, output for each query variant is appended to a text file. If FALSE, output of each query variant is saved in its own text file.

Value

text file(s) are saved to the current working directory.

Examples

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## Not run: snps_to_upload <- c("rs3", "rs4")
## Not run: LDproxy_batch(snp = snps_to_upload, token = Sys.getenv("LDLINK_TOKEN"), append = FALSE)

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