NIH / NCI Genomic Data Commons Access


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Documentation for package ‘GenomicDataCommons’ version 1.32.0

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GenomicDataCommons-package GenomicDataCommons: A package for interfacing with the NCI GDC
aggregations aggregations
aggregations.GDCQuery aggregations
aggregations.GDCResponse aggregations
annotations Start a query of GDC metadata
available_expand Return valid values for "expand"
available_expand.character Return valid values for "expand"
available_expand.GDCQuery Return valid values for "expand"
available_fields S3 Generic to return all GDC fields
available_fields.character S3 Generic to return all GDC fields
available_fields.GDCQuery S3 Generic to return all GDC fields
available_values Find common values for a GDC field
cases Start a query of GDC metadata
cnvs Start a query of GDC metadata
cnv_occurrences Start a query of GDC metadata
count provide count of records in a 'GDCQuery'
count.GDCQuery provide count of records in a 'GDCQuery'
count.GDCResponse provide count of records in a 'GDCQuery'
default_fields S3 Generic to return default GDC fields
default_fields.character S3 Generic to return default GDC fields
default_fields.GDCQuery S3 Generic to return default GDC fields
entity_name Get the entity name from a GDCQuery object
entity_name.GDCQuery Get the entity name from a GDCQuery object
entity_name.GDCResults Get the entity name from a GDCQuery object
expand Set the 'expand' parameter
expand.GDCQuery Set the 'expand' parameter
facet Set facets for a 'GDCQuery'
field_description S3 Generic that returns the field description text, if available
field_description.character S3 Generic that returns the field description text, if available
field_description.GDCQuery S3 Generic that returns the field description text, if available
files Start a query of GDC metadata
filter Manipulating GDCQuery filters
filter.GDCQuery Manipulating GDCQuery filters
filtering Manipulating GDCQuery filters
gdcdata Download GDC files
GDCQuery Start a query of GDC metadata
GDCResponse Fetch 'GDCQuery' metadata from GDC
gdc_cache Work with gdc cache directory
gdc_client return gdc-client executable path
gdc_client_version_validate Bulk data download
gdc_clinical Get clinical information from GDC
gdc_set_cache Work with gdc cache directory
gdc_token return a gdc token from file or environment
genes Start a query of GDC metadata
GenomicDataCommons GenomicDataCommons: A package for interfacing with the NCI GDC
get_facets Set facets for a 'GDCQuery'
get_facets.GDCQuery Set facets for a 'GDCQuery'
get_filter Manipulating GDCQuery filters
get_filter.GDCQuery Manipulating GDCQuery filters
grep_fields Find matching field names
ids Get the ids associated with a GDC query or response
ids.GDCManifest Get the ids associated with a GDC query or response
ids.GDCQuery Get the ids associated with a GDC query or response
ids.GDCResponse Get the ids associated with a GDC query or response
ids.GDCResults Get the ids associated with a GDC query or response
id_field get the name of the id field
id_field.GDCQuery get the name of the id field
id_field.GDCResults get the name of the id field
make_filter Create NCI GDC filters for limiting GDC query results
manifest Prepare GDC manifest file for bulk download
manifest.GDCcasesResponse Prepare GDC manifest file for bulk download
manifest.GDCfilesResponse Prepare GDC manifest file for bulk download
manifest.gdc_files Prepare GDC manifest file for bulk download
mapping Query GDC for available endpoint fields
projects Start a query of GDC metadata
query Start a query of GDC metadata
readDNAcopy Read DNAcopy results into GRanges object
readHTSeqFile Read a single htseq-counts result file.
response Fetch 'GDCQuery' metadata from GDC
response.GDCQuery Fetch 'GDCQuery' metadata from GDC
response_all Fetch 'GDCQuery' metadata from GDC
results results
results.GDCQuery results
results.GDCResponse results
results_all results_all
results_all.GDCQuery results_all
results_all.GDCResponse results_all
select S3 generic to set GDCQuery fields
select.GDCQuery S3 generic to set GDCQuery fields
slicing Query GDC for data slices
ssms Start a query of GDC metadata
ssm_occurrences Start a query of GDC metadata
status Query the GDC for current status
transfer Bulk data download
transfer_help Bulk data download
write_manifest write a manifest data.frame to disk