getVariant: Return the variant object for the given HGVS id.

In myvariant: Accesses MyVariant.info variant query and annotation services

Description

This is a wrapper for GET query of "/variant/<hgvsid>" service.

Usage

getVariant(hgvsid, fields=NULL, 
        ..., return.as=c("records", "text"), myvariant)

Arguments

hgvsid	HGVS id
fields	Fields to return, a list of a comma-sep string. If fields=="all", all available fields are returned.
...
return.as	"records"" (list), "text" (JSON).
myvariant	A MyVariant object that describes how to connect to data resources. See MyVariant-class. If missing, default object will be used that accesses the main MyVariant.info portal. Default is recommended.

Value

returns a variant object containing the queried annotations

References

http://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#get-request http://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#query-parameters

See Also

getVariants queryVariant queryVariants

Examples

## return the variant object for the given HGVS id
getVariant("chr7:g.55241707G>T")

## customize fields
getVariant("chr7:g.55241707G>T", 
          fields=c("dbnsfp.cadd.phred", "dbnsfp.polyphen2"), 
          return.as="text")

myvariant documentation built on Nov. 8, 2020, 5:32 p.m.