# NIH / NCI Genomic Data Commons Access

## Documentation for package ‘GenomicDataCommons’ version 1.25.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
GDC-deprecated | Deprecated functionality in the 'GenomicDataCommons' package
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 | ncigdc: A package for computating the notorious bar statistic.
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
legacy | Deprecated functionality in the 'GenomicDataCommons' package
legacy.GDCQuery | Deprecated functionality in the 'GenomicDataCommons' package
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