ld_matrix_LDLink: Retrieve LD matrix with LDLink
In adamleejohnson/r-tools: AJ's R Tools

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.

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

`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