searchVariants {GA4GHclient} | R Documentation |
Search for variants by genomic ranges (lines of VCF files).
searchVariants(host, variantSetId, referenceName, start, end, callSetIds = character(), nrows = Inf, responseSize = NA_integer_, asVCF = TRUE)
host |
URL of GA4GH API data server. |
variantSetId |
The variant set to search. |
referenceName |
Required. Only return variants on this reference. |
start |
Required. The beginning of the window (1-based, inclusive) for which overlapping variants 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. The end of the window (1-based, inclusive) for which overlapping variants should be returned. |
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 |
asVCF |
If |
This function maps to POST host/variants/search
.
VCF
object (when asVCF = TRUE
) or
DataFrame
object (otherwise).
DataFrame
, getVariant
,
searchVariantsByGRanges
, VCF
,
makeVCFFromGA4GHResponse
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id searchVariants(host, variantSetId, referenceName = "1", start = 15000, end = 16000) searchVariants(host, variantSetId, referenceName = "1", start = 15000, end = 16000, asVCF = FALSE) ## End(Not run)