searchVariantsByGRanges: searchVariantsByGranges function
In labbcb/GA4GHclient: A Bioconductor package for accessing GA4GH API data servers

Description Usage Arguments Details Value References See Also Examples

View source: R/searchVariantsByGRanges.R

Search for variants by genomic ranges (lines of VCF files)

1 2	searchVariantsByGRanges(host, variantSetId, granges, callSetIds = character(), nrows = Inf, responseSize = NA_integer_, asVCF = FALSE)

`host`	URL of GA4GH API data server.
`variantSetId`	The variant set to search.
`granges`	A GRanges object containing one or more genomic ranges.
`callSetIds`	Only return variant calls which belong to callsets with these IDs. If unspecified, return all variants and no variant call objects.
`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.
`asVCF`	If `TRUE` the function will return a list of `VCF` object with headers (default), otherwise it will return a list of `DataFrame` objects.

This function maps to the body of POST host/variants/search.

List of VCF objects (when asVCF = TRUE) or a list of DataFrame objects (otherwise). Each row in GRanges object will be a element of the list.

Official documentation.

DataFrame, searchVariants getVariant, VCF

library(GenomicRanges)
host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id[1]
granges <- GRanges(seqnames = "1", IRanges(start = 15000, end = 16000))
searchVariantsByGRanges(host, variantSetId, granges)

## End(Not run)