| Title: | A Bioconductor package for accessing GA4GH API data servers |
|---|---|
| Description: | GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects. |
| Authors: | Welliton Souza [aut, cre], Benilton Carvalho [ctb], Cristiane Rocha [ctb] |
| Maintainer: | Welliton Souza <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.31.0 |
| Built: | 2024-12-18 04:27:25 UTC |
| Source: | https://github.com/bioc/GA4GHclient |
GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.
Welliton Souza, Benilton Carvalho, Cristiane Rocha
Maintainer: Welliton Souza <[email protected]>
Get a biosample by its ID.
getBiosample(host, biosampleId)getBiosample(host, biosampleId)
host |
URL of GA4GH API data server. |
biosampleId |
ID of the biosample requested. |
This function requests GET host/datasets/biosampleId.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id biosampleId <- searchBiosamples(host, datasetId, nrows = 1)$id getBiosample(host, biosampleId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id biosampleId <- searchBiosamples(host, datasetId, nrows = 1)$id getBiosample(host, biosampleId) ## End(Not run)
Get a call set by its ID.
getCallSet(host, callSetId)getCallSet(host, callSetId)
host |
URL of GA4GH API data server. |
callSetId |
The ID of the CallSet to be retrieved. |
This request maps to GET host/callsets/callSetId.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id callSetId <- searchCallSets(host, variantSetId, nrows = 1)$id getCallSet(host, callSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id callSetId <- searchCallSets(host, variantSetId, nrows = 1)$id getCallSet(host, callSetId) ## End(Not run)
Get a dataset by its ID.
getDataset(host, datasetId)getDataset(host, datasetId)
host |
URL of GA4GH API data server. |
datasetId |
The ID of the dataset to be retrieved. |
This function requests GET host/datasets/datasetId.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id getDataset(host, datasetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id getDataset(host, datasetId) ## End(Not run)
Get an expression level by its ID.
getExpressionLevel(host, expressionLevelId)getExpressionLevel(host, expressionLevelId)
host |
URL of GA4GH API data server. |
expressionLevelId |
ID of the expression level. |
This function requests GET host/expressionlevels/expressionLevelId.
DataFrame object.
DataFrame, searchExpressionLevels
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrow = 1)$id rnaQuantificationId <- searchRnaQuantifications(host, rnaQuantificationSetId, nrows = 1)$id expressionLevelId <- searchExpressionLevels(host, rnaQuantificationId, nrows = 1)$id getExpressionLevel(host, expressionLevelId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrow = 1)$id rnaQuantificationId <- searchRnaQuantifications(host, rnaQuantificationSetId, nrows = 1)$id expressionLevelId <- searchExpressionLevels(host, rnaQuantificationId, nrows = 1)$id getExpressionLevel(host, expressionLevelId) ## End(Not run)
Get a feature set by its ID (a line of genomic feature file).
getFeature(host, featureId)getFeature(host, featureId)
host |
URL of GA4GH API data server. |
featureId |
The ID of the feature to be retrieved. |
This function requests GET host/features/featureId.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id featureSetId <- searchFeatureSets(host, datasetId, nrows = 1)$id featureId <- searchFeatures(host, featureSetId, nrows = 1)$id getFeature(host, featureId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id featureSetId <- searchFeatureSets(host, datasetId, nrows = 1)$id featureId <- searchFeatures(host, featureSetId, nrows = 1)$id getFeature(host, featureId) ## End(Not run)
Get a feature set by its ID.
getFeatureSet(host, featureSetId)getFeatureSet(host, featureSetId)
host |
URL of GA4GH API data server. |
featureSetId |
The ID of the FeatureSet to be retrieved. |
This function requests GET host/featuresets/featureSetId.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id featureSetId <- searchFeatureSets(host, datasetId, nrows = 1)$id getFeatureSet(host, featureSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id featureSetId <- searchFeatureSets(host, datasetId, nrows = 1)$id getFeatureSet(host, featureSetId) ## End(Not run)
Get an individual by its ID.
getIndividual(host, individualId)getIndividual(host, individualId)
host |
URL of GA4GH API data server. |
individualId |
ID of the individual requested. |
This function requests GET host/individuals/individualId.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id individualId <- searchIndividuals(host, datasetId, nrows = 1)$id getIndividual(host, individualId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id individualId <- searchIndividuals(host, datasetId, nrows = 1)$id getIndividual(host, individualId) ## End(Not run)
Get a read group set by its ID.
getReadGroupSet(host, readGroupSetId)getReadGroupSet(host, readGroupSetId)
host |
URL of GA4GH API data server. |
readGroupSetId |
The ID of the ReadGroupSet to be retrieved. |
This function requests GET host/readgroupsets/readGroupSetId.
DataFrame object.
DataFrame, searchReadGroupSets
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id readGroupSetId <- searchReadGroupSets(host, datasetId, nrows = 1)$id getReadGroupSet(host, readGroupSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id readGroupSetId <- searchReadGroupSets(host, datasetId, nrows = 1)$id getReadGroupSet(host, readGroupSetId) ## End(Not run)
Get a reference by its ID.
getReference(host, referenceId)getReference(host, referenceId)
host |
URL of GA4GH API data server. |
referenceId |
The ID of the Reference to be retrieved. |
This function requests GET host/references/referenceId.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id getReference(host, referenceId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id getReference(host, referenceId) ## End(Not run)
Get a reference set by its ID.
getReferenceSet(host, referenceSetId)getReferenceSet(host, referenceSetId)
host |
URL of GA4GH API data server. |
referenceSetId |
The ID of the ReferenceSet to be retrieved. |
This function requests GET host/referencesets/referenceSetId.
DataFrame object.
DataFrame, searchReferenceSets
host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id getReferenceSet(host, referenceSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id getReferenceSet(host, referenceSetId) ## End(Not run)
Get an RNA quantification by its ID.
getRnaQuantification(host, rnaQuantificationId)getRnaQuantification(host, rnaQuantificationId)
host |
URL of GA4GH API data server. |
rnaQuantificationId |
ID of the RNA quantification requested. |
This function requests GET host/rnaquantifications/rnaQuantificationId.
DataFrame object.
DataFrame, searchRnaQuantifications
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrows = 1)$id rnaQuantificationId <- searchRnaQuantifications(host, rnaQuantificationSetId, nrows = 1)$id getRnaQuantification(host, rnaQuantificationId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrows = 1)$id rnaQuantificationId <- searchRnaQuantifications(host, rnaQuantificationSetId, nrows = 1)$id getRnaQuantification(host, rnaQuantificationId) ## End(Not run)
Get an RNA quantification set by its ID.
getRnaQuantificationSet(host, rnaQuantificationSetId)getRnaQuantificationSet(host, rnaQuantificationSetId)
host |
URL of GA4GH API data server. |
rnaQuantificationSetId |
ID of the RNA quantification set requested. |
This function requests GET host/rnaquantificationsets/rnaQuantificationSetId.
DataFrame object.
DataFrame, searchRnaQuantificationSets
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrows = 1)$id getRnaQuantificationSet(host, rnaQuantificationSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrows = 1)$id getRnaQuantificationSet(host, rnaQuantificationSetId) ## End(Not run)
Get a variant by its ID with all call sets for this variant.
getVariant(host, variantId, asVCF = TRUE)getVariant(host, variantId, asVCF = TRUE)
host |
URL of GA4GH API data server. |
variantId |
The ID of the Variant to be retrieved. |
asVCF |
If |
This function requests GET host/variants/variantId.
VCF object (when asVCF = TRUE) or
DataFrame object (otherwise).
DataFrame, searchVariants,
searchVariantsByGRanges, VCF,
makeVCFFromGA4GHResponse
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id variantId <- searchVariants(host, variantSetId, "1", 15031, 15031)$id getVariant(host, variantId) getVariant(host, variantId, asVCF = FALSE) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id variantId <- searchVariants(host, variantSetId, "1", 15031, 15031)$id getVariant(host, variantId) getVariant(host, variantId, asVCF = FALSE) ## End(Not run)
Get a variant annotation set by its ID.
getVariantAnnotationSet(host, variantAnnotationSetId)getVariantAnnotationSet(host, variantAnnotationSetId)
host |
URL of GA4GH API data server. |
variantAnnotationSetId |
ID of variant annotation set. |
This function requests
GET host/variantannotationsets/variantAnnotationSetId.
DataFrame object.
DataFrame,
searchVariantAnnotationSets
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)$id getVariantAnnotationSet(host, variantAnnotationSetId = id) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 2)$id[2] id <- searchVariantAnnotationSets(host, variantSetId, nrows = 1)$id getVariantAnnotationSet(host, variantAnnotationSetId = id) ## End(Not run)
Get a variant set by its ID.
getVariantSet(host, variantSetId, asVCFHeader = TRUE)getVariantSet(host, variantSetId, asVCFHeader = TRUE)
host |
URL of GA4GH API data server. |
variantSetId |
The ID of the VariantSet to be retrieved. |
asVCFHeader |
If |
This function requests GET host/variantsets/variantSetId.
DataFrame object. It can be converted
into VCFHeader object.
DataFrame, searchVariantSets,
VCFHeader, makeVCFHeaderFromGA4GHResponse
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id getVariantSet(host, variantSetId) getVariantSet(host, variantSetId, asVCF = FALSE) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id getVariantSet(host, variantSetId) getVariantSet(host, variantSetId, asVCF = FALSE) ## End(Not run)
This function follows the official reference HGVS nomenclature. At this moment, it supports only 'substitution' and 'indel' for DNA sequences.
HGVSnames(start, ref, alt, type = "g", seqnames = NA_character_)HGVSnames(start, ref, alt, type = "g", seqnames = NA_character_)
start |
genomic location of start |
ref |
reference sequence |
alt |
alternate sequence |
type |
Sequence type to be used as prefix. Allowed options are:
|
seqnames |
name of sequence (e.g. chr1, 1). It is optional. |
Genomic coordinates of variants formatted as HGVS nomenclature.
Sequence Variant Nomenclature.
start <- c(45576, "88+1", 6775, 6775, 145, 9002, 4, 12345611, 58347698) ref <- c("A", "G", "T", "TCA", "CGA", "AAAAAAAA", "GC", "G", "A") alt <- c("C", "T", "GA", "C", "TGG", "TTT", "TG", "A", "*") type <- c("g", "c", "g", "g", "c", "g", "g", "g", "g") seqnames <- c("", "", NA, NA, NA, NA, NA, "chr11", NA) HGVSnames(start, ref, alt, type, seqnames)start <- c(45576, "88+1", 6775, 6775, 145, 9002, 4, 12345611, 58347698) ref <- c("A", "G", "T", "TCA", "CGA", "AAAAAAAA", "GC", "G", "A") alt <- c("C", "T", "GA", "C", "TGG", "TTT", "TG", "A", "*") type <- c("g", "c", "g", "g", "c", "g", "g", "g", "g") seqnames <- c("", "", NA, NA, NA, NA, NA, "chr11", NA) HGVSnames(start, ref, alt, type, seqnames)
Get the sequence bases of a reference genome by genomic range.
listReferenceBases(host, referenceId, start = 1, end = NA_integer_)listReferenceBases(host, referenceId, start = 1, end = NA_integer_)
host |
URL of GA4GH API data server. |
referenceId |
The ID of the Reference to be retrieved. |
start |
The start position (1-based) of this query. Defaults to 0. 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 |
The end position (1-based, inclusive) of this query. Defaults to the length of this Reference. |
This function requests POST host/listreferencebases.
BString object.
searchReferenceSets, searchReferences
host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id listReferenceBases(host, referenceId, start = 1, end = 100) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id listReferenceBases(host, referenceId, start = 1, end = 100) ## End(Not run)
Convert DataFrame output from
searchVariants and getVariant functions to
VCF class.
makeVCFFromGA4GHResponse(variants)makeVCFFromGA4GHResponse(variants)
variants |
|
VCF object.
searchVariants, getVariant,
VCF, DataFrame
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id variants <- searchVariants(host, variantSetId, referenceName = "1", start = 15000, end = 16000) variants makeVCFFromGA4GHResponse(variants) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id variants <- searchVariants(host, variantSetId, referenceName = "1", start = 15000, end = 16000) variants makeVCFFromGA4GHResponse(variants) ## End(Not run)
Convert DataFrame output from
getVariantSet function to VCFHeader class.
makeVCFHeaderFromGA4GHResponse(variantSet)makeVCFHeaderFromGA4GHResponse(variantSet)
variantSet |
|
VCFHeader object.
getVariantSet, VCFHeader,
DataFrame
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id variantId <- searchVariants(host, variantSetId, "1", 15031, 15031)$id variant <- getVariant(host, variantId) makeVCFFromGA4GHResponse(variant) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id variantId <- searchVariants(host, variantSetId, "1", 15031, 15031)$id variant <- getVariant(host, variantId) makeVCFFromGA4GHResponse(variant) ## End(Not run)
This function gets Biosamples matching the search criteria.
searchBiosamples(host, datasetId, name = NA_character_, individualId = NA_character_, nrows = Inf, responseSize = NA_integer_)searchBiosamples(host, datasetId, name = NA_character_, individualId = NA_character_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
datasetId |
Id of the dataset to search. |
name |
Returns Biosamples with the given name found by case-sensitive string matching. |
individualId |
Returns Biosamples for the provided individual ID. |
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 |
This function requests to /biosamples/search.
DataFrame object. NULL means no registry found.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchBiosamples(host, datasetId, nrows = 10) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchBiosamples(host, datasetId, nrows = 10) ## End(Not run)
Search for call sets (sample columns of VCF files).
searchCallSets(host, variantSetId, name = NA_character_, biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)searchCallSets(host, variantSetId, name = NA_character_, biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
variantSetId |
The VariantSet to search. |
name |
Only return call sets with this name (case-sensitive, exact match). |
biosampleId |
Return only call sets generated from the provided BioSample ID. |
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 |
This function requests POST host/callsets/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id searchCallSets(host, variantSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id searchCallSets(host, variantSetId) ## End(Not run)
Search for datasets.
searchDatasets(host, nrows = Inf, responseSize = NA_integer_)searchDatasets(host, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
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 |
This function requests to POST /datasets/search.
DataFrame object. NULL means no registry found.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: searchDatasets(host) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: searchDatasets(host) ## End(Not run)
This function gets expression levels matching the search criteria.
searchExpressionLevels(host, rnaQuantificationId, nrows = Inf, responseSize = NA_integer_)searchExpressionLevels(host, rnaQuantificationId, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
rnaQuantificationId |
Id of the rnaQuantification to restrict search to. |
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 |
This function requests to /expressionlevels/search.
DataFrame object. NULL means no registry found.
DataFrame, getExpressionLevel,
searchRnaQuantificationSets
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrow = 1)$id rnaQuantificationId <- searchRnaQuantifications(host, rnaQuantificationSetId, nrows = 1)$id searchExpressionLevels(host, rnaQuantificationId, nrows = 10) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id rnaQuantificationSetId <- searchRnaQuantificationSets(host, datasetId, nrow = 1)$id rnaQuantificationId <- searchRnaQuantifications(host, rnaQuantificationSetId, nrows = 1)$id searchExpressionLevels(host, rnaQuantificationId, nrows = 10) ## End(Not run)
Search for features (lines of genomic feature files).
searchFeatures(host, featureSetId, name = NA_character_, geneSymbol = NA_character_, parentId = NA_character_, referenceName = NA_character_, start = NA_integer_, end = NA_integer_, featureTypes = character(), nrows = Inf, responseSize = NA_integer_)searchFeatures(host, featureSetId, name = NA_character_, geneSymbol = NA_character_, parentId = NA_character_, referenceName = NA_character_, start = NA_integer_, end = NA_integer_, featureTypes = character(), nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
featureSetId |
The annotation set to search within. Either featureSetId or parentId must be non-empty. |
name |
Only returns features with this name (case-sensitive, exact match). |
geneSymbol |
Only return features with matching the provided gene symbol (case-sensitive, exact match). This field may be replaced with a more generic representation in a future version. |
parentId |
Restricts the search to direct children of the given parent feature ID. Either feature_set_id or parent_id must be non-empty. |
referenceName |
Only return features on the reference with this name (matched to literal reference name as imported from the GFF3). |
start |
Required, if name or symbol not provided. The beginning of the window (0-based, inclusive) for which overlapping features 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 0). |
end |
Required, if name or symbol not provided. The end of the window (0-based, exclusive) for which overlapping features should be returned. |
featureTypes |
TODO: To be replaced with a fully featured ontology search once the Metadata definitions are rounded out. If specified, this query matches only annotations whose feature_type matches one of the provided ontology terms. |
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 |
This function requests POST host/features/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id featureSetId <- searchFeatureSets(host, datasetId, nrows = 1)$id searchFeatures(host, featureSetId, nrows = 10) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id featureSetId <- searchFeatureSets(host, datasetId, nrows = 1)$id searchFeatures(host, featureSetId, nrows = 10) ## End(Not run)
Search for feature sets (genomic features, e.g. GFF files).
searchFeatureSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)searchFeatureSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
datasetId |
The Dataset to search. |
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 |
This function requests POST host/featuresets/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchFeatureSets(host, datasetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchFeatureSets(host, datasetId) ## End(Not run)
This function gets individuals matching the search criteria.
searchIndividuals(host, datasetId, name = NA_character_, nrows = Inf, responseSize = NA_integer_)searchIndividuals(host, datasetId, name = NA_character_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
datasetId |
Id of the dataset to search. |
name |
Returns Individuals with the given name found by case-sensitive string matching. |
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 |
This function requests to /individuals/search.
DataFrame object. NULL means no registry found.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchIndividuals(host, datasetId, nrows = 10) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchIndividuals(host, datasetId, nrows = 10) ## End(Not run)
This function gets a list of phenotype associations matching the search criteria.
searchPhenotypeAssociations(host, phenotypeAssociationSetId, featureIds = character(), phenotypeIds = character(), nrows = Inf, responseSize = NA_integer_)searchPhenotypeAssociations(host, phenotypeAssociationSetId, featureIds = character(), phenotypeIds = character(), nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
phenotypeAssociationSetId |
Id of the PhenotypeAssociationSet to search. |
featureIds |
Ids of the features. At least one |
phenotypeIds |
Ids of the phenotypes. At least one |
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 |
This function requests to /featurephenotypeassociations/search.
DataFrame object. NULL means no registry found.
DataFrame, searchPhenotypeAssociationSets
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id id <- searchPhenotypeAssociationSets(host, datasetId, nrows = 1)$id searchPhenotypeAssociations(host, id, nrows = 10) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id id <- searchPhenotypeAssociationSets(host, datasetId, nrows = 1)$id searchPhenotypeAssociations(host, id, nrows = 10) ## End(Not run)
This function gets a list of association sets matching the search criteria.
searchPhenotypeAssociationSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)searchPhenotypeAssociationSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
datasetId |
Id of the dataset to search. |
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 |
This function requests to /phenotypeassociationsets/search.
DataFrame object. NULL means no registry found.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchPhenotypeAssociationSets(host, datasetId, nrows = 10) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchPhenotypeAssociationSets(host, datasetId, nrows = 10) ## End(Not run)
Search for read group sets (sequence alignement, e.g BAM files).
searchReadGroupSets(host, datasetId, name = NA_character_, biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)searchReadGroupSets(host, datasetId, name = NA_character_, biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
datasetId |
The dataset to search. |
name |
Only return read group sets with this name (case-sensitive, exact match). |
biosampleId |
Specifying the id of a BioSample record will return only readgroups with the given biosampleId. |
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 |
This function requests POST host/readgroupsets/search
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchReadGroupSets(host, datasetId, nrows = 1) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchReadGroupSets(host, datasetId, nrows = 1) ## End(Not run)
Search for reads by genomic range (bases of aligned sequences)
searchReads(host, readGroupIds, referenceId = NA_character_, start = NA_integer_, end = NA_integer_, nrows = Inf, responseSize = NA_integer_)searchReads(host, readGroupIds, referenceId = NA_character_, start = NA_integer_, end = NA_integer_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
readGroupIds |
The ReadGroups to search. At least one id must be specified. |
referenceId |
The reference to query. Leaving blank returns results from all references, including unmapped reads - this could be very large. |
start |
The start position (1-based) of this query. If a reference is specified, this defaults to 0. 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 |
The end position (1-based, exclusive) of this query. If a reference is specified, this defaults to the reference's length. |
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 |
This function requests POST host/reads/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: readGroupIds <- "WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIiwiRVJSMTgxMzI5Il0" referenceSetId <- searchReferenceSets(host, nrows = 1)$id referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id searchReads(host, readGroupIds, referenceId, start = 15000, end = 16000) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: readGroupIds <- "WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIiwiRVJSMTgxMzI5Il0" referenceSetId <- searchReferenceSets(host, nrows = 1)$id referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id searchReads(host, readGroupIds, referenceId, start = 15000, end = 16000) ## End(Not run)
Search for references (genome sequences, e.g. chromosomes).
searchReferences(host, referenceSetId, md5checksum = NA_character_, accession = NA_character_, nrows = Inf, responseSize = NA_integer_)searchReferences(host, referenceSetId, md5checksum = NA_character_, accession = NA_character_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
referenceSetId |
The ReferenceSet to search. |
md5checksum |
If specified, return the references for which the md5checksum matches this string (case-sensitive, exact match). See ReferenceSet::md5checksum for details. |
accession |
If specified, return the references for which the accession matches this string (case-sensitive, exact match). |
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 |
This function requests POST host/references/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id searchReferences(host, referenceSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: referenceSetId <- searchReferenceSets(host, nrows = 1)$id searchReferences(host, referenceSetId) ## End(Not run)
Search for reference sets (reference genomes).
searchReferenceSets(host, md5checksum = NA_character_, accession = NA_character_, assemblyId = NA_character_, nrows = Inf, responseSize = NA_integer_)searchReferenceSets(host, md5checksum = NA_character_, accession = NA_character_, assemblyId = NA_character_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
md5checksum |
If unset, return the reference sets for which the md5checksum matches this string (case-sensitive, exact match). See ReferenceSet::md5checksum for details. |
accession |
If unset, return the reference sets for which the accession matches this string (case-sensitive, exact match). |
assemblyId |
If unset, return the reference sets for which the assemblyId matches this string (case-sensitive, exact match). |
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 |
This function requests POST host/references/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: searchReferenceSets(host) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: searchReferenceSets(host) ## End(Not run)
This function gets a list of RnaQuantifications matching the search criteria.
searchRnaQuantifications(host, rnaQuantificationSetId, biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)searchRnaQuantifications(host, rnaQuantificationSetId, biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
rnaQuantificationSetId |
IReturn only Rna Quantifications which belong to this set. |
biosampleId |
Return only RNA quantifications regarding the specified biosample. |
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 |
This function requests to /rnaquantifications/search.
DataFrame object. NULL means no registry found.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id id <- searchRnaQuantificationSets(host, datasetId, nrows = 1)$id searchRnaQuantifications(host, rnaQuantificationSetId = id) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id id <- searchRnaQuantificationSets(host, datasetId, nrows = 1)$id searchRnaQuantifications(host, rnaQuantificationSetId = id) ## End(Not run)
This function gets a list of RNA quantification sets matching the search criteria.
searchRnaQuantificationSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)searchRnaQuantificationSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
datasetId |
Id of the dataset to search. |
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 |
This function requests to /rnaquantificationsets/search.
DataFrame object. NULL means no registry found.
DataFrame, getRnaQuantificationSet
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchRnaQuantificationSets(host, datasetId, nrows = 1) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchRnaQuantificationSets(host, datasetId, nrows = 1) ## End(Not run)
Search for annotated variants by genomic range.
searchVariantAnnotations(host, variantAnnotationSetId, referenceName = NA_character_, referenceId = NA_character_, start = NA_integer_, end = NA_integer_, effects = list(), nrows = Inf, responseSize = NA_integer_)searchVariantAnnotations(host, variantAnnotationSetId, referenceName = NA_character_, referenceId = NA_character_, start = NA_integer_, end = NA_integer_, effects = list(), nrows = Inf, responseSize = NA_integer_)
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 |
This function requests POST host/variantannotations/search.
DataFrame object.
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)$id searchVariantAnnotations(host, variantAnnotationSetId = id, referenceName = "1", start = 15000, end = 16000) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$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)
Search for variant annotation sets (annotated VCF files).
searchVariantAnnotationSets(host, variantSetId, nrows = Inf, responseSize = NA_integer_)searchVariantAnnotationSets(host, variantSetId, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
variantSetId |
Required. The VariantSet to search. |
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 |
This function maps to POST host/variantannotationsets/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 2)$id[2] searchVariantAnnotationSets(host, variantSetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id variantSetId <- searchVariantSets(host, datasetId, nrows = 2)$id[2] searchVariantAnnotationSets(host, variantSetId) ## End(Not run)
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)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)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)
Search for variants by genomic ranges (lines of VCF files)
searchVariantsByGRanges(host, variantSetId, granges, callSetIds = character(), nrows = Inf, responseSize = NA_integer_, asVCF = FALSE)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 |
asVCF |
If |
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.
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)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)
Search for for variant sets (VCF files).
searchVariantSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)searchVariantSets(host, datasetId, nrows = Inf, responseSize = NA_integer_)
host |
URL of GA4GH API data server. |
datasetId |
Id of the dataset to search. |
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 |
This request maps to the body of POST host/variantsets/search.
DataFrame object.
host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchVariantSets(host, datasetId) ## End(Not run)host <- "http://1kgenomes.ga4gh.org/" ## Not run: datasetId <- searchDatasets(host, nrows = 1)$id searchVariantSets(host, datasetId) ## End(Not run)