SNPclip {LDlinkR}

Prune a list of variants by linkage disequilibrium.

Description

Prune a list of variants by linkage disequilibrium.

Usage

SNPclip(
  snps,
  pop = "CEU",
  r2_threshold = "0.1",
  maf_threshold = "0.01",
  token = NULL,
  file = FALSE,
  genome_build = "grch37",
  api_root = "https://ldlink.nih.gov/LDlinkRest"
)

Arguments

snps

a list of between 1 - 5,000 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"

r2_threshold

LD R2 threshold between 0-1, default = 0.1

maf_threshold

minor allele frequency threshold between 0-1, default = 0.01

token

LDlink provided user token, default = NULL, register for token at https://ldlink.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.

genome_build

Choose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19).

api_root

Optional alternative root url for API.

Value

a data frame

Examples

## Not run: SNPclip(c("rs3", "rs4", "rs148890987"), "YRI", "0.1", "0.01",
                    token = Sys.getenv("LDLINK_TOKEN"))
                 
## End(Not run)