ld_matrix_LDLink: Retrieve LD matrix with LDLink

In adamleejohnson/R-ajtools: AJ's R Tools

Retrieve LD matrix with LDLink

Description

This function is a wrapper around LDlinkR::LDmatrix() that allows queries for greater than 1000 SNPs, and using an optional local cache file for faster look-ups. The LDlink API only allows queries of up to 1000s SNPs at a time. This function makes repeated calls to the API to build the appropriate LD matrix.

Usage

ld_matrix_LDLink(
  snps,
  pop = "EUR",
  r2d = "r2",
  tokens = NULL,
  cache = NULL,
  cache_tokens = TRUE,
  max_query_size = 1000,
  progress = TRUE,
  compress = FALSE
)

Arguments

snps	List of variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446")
pop	A 1000 Genomes Project population, default = "EUR"
r2d	Either "r2" for LD R2 or "d" for LD D', default = "r2"
tokens	List of LDLink tokens. If multiple tokens are provided, look-ups will be performed in parallel
cache	Name of an optional cache file to read/store results from/to
cache_tokens	Whether to save tokens in the exported LD cache file.
max_query_size	Max number of SNPs to pass to LDlinkR at a time
progress	Display a progress indicator
compress	Whether output rds should be compressed

adamleejohnson/R-ajtools documentation built on April 4, 2022, 7:24 a.m.