Description Usage Arguments Value
Makes a query to the NCBI webservice to fetch the ClinVar entries for the given gene and filters them down to missense variants
1 2 | fetchClinvar(gene, stagger = TRUE, overrideCache = FALSE,
logger = NULL)
|
gene |
gene name as in ClinVar (e.g. 'CALM1') |
stagger |
logical determining whether HTTP requests should be staggered by a third of a second to avoid rejection by the server. Defaults to TRUE. |
overrideCache |
logical determining whether local cache should be overridden |
logger |
a yogilogger object to write log messages to. Defaults to NULL |
a data.frame
with the following columns:
hgvsc
The HGVS variant descriptor at the coding sequence (DNA) level
hgvsp
The HGVS variant descriptor at the amino acid sequence (Protein) level
clinsig
The ClinVar clinical significance string (e.g "Likely pathogenic")
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