Downloads either the current ClinVar release or a named monthly archive from
the NCBI HTTPS service. The flat reports are the compact default input to
rclinvarbitration_import_flat(). VCV XML feeds the same scalar clinvar
table when an analysis also needs observations, citations, conditions,
attributes, or attributable text that the flat reports do not contain.
Usage
rclinvarbitration_download_clinvar(
release = "latest",
file = "vcv_xml",
cache_dir = tools::R_user_dir("RClinVarbitration", "cache"),
overwrite = FALSE,
quiet = FALSE
)Arguments
- release
"latest"or a monthly archive in"YYYY-MM"form.- file
One or more of
"vcv_xml","submission_summary", and"variant_summary".- cache_dir
Directory in which downloaded files are cached.
- overwrite
Download even when a valid cached file is present?
- quiet
Passed to
utils::download.file().
Value
A named character vector of local paths. The download attribute is
a data frame containing source URLs, MD5 values when available, and cache
hit status.
Details
Existing files form a local cache. Current files and archived VCV XML files
are checked against NCBI's MD5 sidecar; a matching file is reused and a stale
or corrupt file is replaced only after a temporary download is verified.
NCBI does not publish MD5 sidecars
beside archived flat files, so those files are reused by name unless
overwrite = TRUE.
A complete VCV release is several gigabytes. The default cache location is
returned by tools::R_user_dir("RClinVarbitration", "cache"). The function
raises R's download timeout to at least the value of option
RClinVarbitration.download_timeout (7200 seconds by default) for the call.