Function reference • GenomicDataCommons

All functions

GenomicDataCommons: ncigdc: A package for computating the notorious bar statistic.

aggregations(): aggregations

available_expand(): Return valid values for "expand"

available_fields(): S3 Generic to return all GDC fields

available_values(): Find common values for a GDC field

count(): provide count of records in a GDCQuery

default_fields(): S3 Generic to return default GDC fields

entity_name(): Get the entity name from a GDCQuery object

expand(): Set the expand parameter

facet() get_facets(): Set facets for a GDCQuery

field_description(): S3 Generic that returns the field description text, if available

filter() get_filter(): Manipulating GDCQuery filters

gdc_cache() gdc_set_cache(): Work with gdc cache directory

gdc_client(): return gdc-client executable path

gdc_clinical(): Get clinical information from GDC

gdc_token(): return a gdc token from file or environment

gdcdata(): Download GDC files

grep_fields(): Find matching field names

id_field(): get the name of the id field

ids(): Get the ids associated with a GDC query or response

legacy(): Set the legacy parameter

make_filter(): Create NCI GDC filters for limiting GDC query results

manifest(): Prepare GDC manifest file for bulk download

mapping(): Query GDC for available endpoint fields

query() cases() files() projects() annotations() ssms() ssm_occurrences() cnvs() cnv_occurrences() genes(): Start a query of GDC metadata

readDNAcopy(): Read DNAcopy results into GRanges object

readHTSeqFile(): Read a single htseq-counts result file.

response() response_all(): Fetch GDCQuery metadata from GDC

results(): results

results_all(): results_all

select(): S3 generic to set GDCQuery fields

slicing(): Query GDC for data slices

status(): Query the GDC for current status

transfer() gdc_client_version_validate() transfer_help(): Bulk data download

write_manifest(): write a manifest data.frame to disk