searchVariantAnnotations: searchVariantAnnotations function

In GA4GHclient: A Bioconductor package for accessing GA4GH API data servers

Description

Search for annotated variants by genomic range.

Usage

searchVariantAnnotations(host, variantAnnotationSetId,
  referenceName = NA_character_, referenceId = NA_character_,
  start = NA_integer_, end = NA_integer_, effects = list(), nrows = Inf,
  responseSize = NA_integer_)

Arguments

host	URL of GA4GH API data server.
variantAnnotationSetId	Required. The ID of the variant annotation set to search over.
referenceName	Only return variants with reference alleles on the reference with this name. One of this field or reference_id is required.
referenceId	Only return variants with reference alleles on the reference with this ID. One of this field or reference_name is required.
start	Required if reference_name or reference_id supplied. The beginning of the window (1-based, inclusive) for which variants with overlapping reference alleles should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 1).
end	Required if reference_name or reference_id supplied. The end of the window (1-based, exclusive) for which variants with overlapping reference alleles should be returned.
effects	This filter allows variant, transcript combinations to be extracted by effect type(s). Only return variant annotations including any of these effects and only return transcript effects including any of these effects. Exact matching across all fields of the Sequence Ontology OntologyTerm is required. (A transcript effect may have multiple SO effects which will all be reported.) If empty, return all variant annotations.
nrows	Number of rows of the data frame returned by this function. If not defined, the function will return all entries. If the number of available entries is less than the value of this this parameter, the function will silently return only the available entries.
responseSize	Specifies the number of entries to be returned by the server until reach the number of rows defined in nrows parameter or until get all available entries. If not defined, the server will return the allowed maximum reponse size. Increasing this the value of this parameter will reduce the number of requests and reducing the time required. The will not respect this parameter if the value if larger than its maximum response size.

Details

This function requests POST host/variantannotations/search.

Value

DataFrame object.

References

Official documentation.

See Also

DataFrame

Examples

host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 2)$id[2]
id <- searchVariantAnnotationSets(host, variantSetId, nrows = 1)$id
searchVariantAnnotations(host, variantAnnotationSetId = id,
    referenceName = "1", start = 15000, end = 16000)

## End(Not run)

GA4GHclient documentation built on Nov. 8, 2020, 5:47 p.m.