brapi_post_variantsets_extract: post /variantsets/extract

In mverouden/brapir-v2: Client to Access BrAPI Compliant Plant Breeding Databases

post /variantsets/extract

Description

Create new VariantSet based on search results

Usage

brapi_post_variantsets_extract(
  con = NULL,
  callSetDbIds = "",
  expandHomozygotes = NA,
  sepPhased = "",
  sepUnphased = "",
  studyDbIds = "",
  studyNames = "",
  unknownString = "",
  variantDbIds = "",
  variantSetDbIds = ""
)

Arguments

con	list; required: TRUE; BrAPI connection object
callSetDbIds	vector of type character; required: FALSE; The CallSet unique database identifier(s) to search.; default: "", when using multiple values supply as c("value1", "value2").
expandHomozygotes	logical; required: FALSE; Should homozygotes be expanded (TRUE) or collapsed into a single occurrence (FALSE); default: NA , other possible values: TRUE | FALSE.
sepPhased	character; required: FALSE; The string used as a separator for phased allele calls.; default: "".
sepUnphased	character; required: FALSE; The string used as a separator for unphased allele calls.; default: "".
studyDbIds	vector of type character; required: FALSE; List of unique database study identifiers to search for; default: "", when using multiple values supply as c("value1", "value2").
studyNames	vector of type character; required: FALSE; List of study names to filter search results; default: "", when using multiple values supply as c("value1", "value2").
unknownString	character; required: FALSE; The string used as a representation for missing data.; default: "".
variantDbIds	vector of type character; required: FALSE; The unique variant database identifiers to search.; default: "", when using multiple values supply as c("value1", "value2").
variantSetDbIds	vector of type character; required: FALSE; The unique VariantSet database identifiers to search.; default: "", when using multiple values supply as c("value1", "value2").

Details

Will perform a search for Calls which match the search criteria in the request made. The results of the search will be used to create a new VariantSet on the server. The new VariantSet will be returned.

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

See Also

Other brapi-genotyping: brapi_get_callsets_callSetDbId_calls(), brapi_get_callsets_callSetDbId(), brapi_get_callsets(), brapi_get_calls(), brapi_get_maps_mapDbId_linkagegroups(), brapi_get_maps_mapDbId(), brapi_get_maps(), brapi_get_markerpositions(), brapi_get_references_referenceDbId_bases(), brapi_get_references_referenceDbId(), brapi_get_referencesets_referenceSetDbId(), brapi_get_referencesets(), brapi_get_references(), brapi_get_samples_sampleDbId(), brapi_get_samples(), brapi_get_search_calls_searchResultsDbId(), brapi_get_search_callsets_searchResultsDbId(), brapi_get_search_markerpositions_searchResultsDbId(), brapi_get_search_references_searchResultsDbId(), brapi_get_search_referencesets_searchResultsDbId(), brapi_get_search_samples_searchResultsDbId(), brapi_get_search_variants_searchResultsDbId(), brapi_get_search_variantsets_searchResultsDbId(), brapi_get_variants_variantDbId_calls(), brapi_get_variants_variantDbId(), brapi_get_variantsets_variantSetDbId_callsets(), brapi_get_variantsets_variantSetDbId_calls(), brapi_get_variantsets_variantSetDbId_variants(), brapi_get_variantsets_variantSetDbId(), brapi_get_variantsets(), brapi_get_variants(), brapi_get_vendor_orders_orderId_plates(), brapi_get_vendor_orders_orderId_results(), brapi_get_vendor_orders_orderId_status(), brapi_get_vendor_orders(), brapi_get_vendor_specifications(), brapi_post_samples(), brapi_post_search_callsets(), brapi_post_search_calls(), brapi_post_search_markerpositions(), brapi_post_search_referencesets(), brapi_post_search_references(), brapi_post_search_samples(), brapi_post_search_variantsets(), brapi_post_search_variants(), brapi_put_samples_sampleDbId()

Other Variant Sets: brapi_get_search_variantsets_searchResultsDbId(), brapi_get_variantsets_variantSetDbId_callsets(), brapi_get_variantsets_variantSetDbId_calls(), brapi_get_variantsets_variantSetDbId_variants(), brapi_get_variantsets_variantSetDbId(), brapi_get_variantsets(), brapi_post_search_variantsets()

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
brapi_post_variantsets_extract(con = con,
                               expandHomozygotes = TRUE,
                               sepPhased = "/",
                               sepUnphased = "|",
                               unknownString = "-",
                               variantDbIds = c("variant01",
                                                "variant02"))

## End(Not run)

mverouden/brapir-v2 documentation built on April 22, 2022, 9:24 a.m.