tcga_dataset_to_data_pool: Add TCGA cohort to data pool

In CCICB/CRUX: Easily explore patterns of somatic variation in cancer using 'CRUX'

Add TCGA cohort to data pool

Description

Takes a TCGA study abbreviation, creates a tcga_dataset_to_maf_dataset_wrapper object for the relevant dataset and adds the wrapper to the maf_data_pool

Usage

tcga_dataset_to_data_pool(
  tcga_study_abbreviation,
  maf_data_pool,
  source = "Firehose"
)

Arguments

tcga_study_abbreviation	a TCGA cohort abbreviation (see maftools::tcgaAvailable()) (string)
maf_data_pool	the data pool to add the dataset wrapper to (maf_data_pool)
source	'MC3' or 'Firehose'. Source of TCGA data to use. See ?maftools::tcgaLoad for details (string)

Value

returns a data pool object with extra dataset added (maf_data_pool)

See Also

Other DataToWrapper: tcga_dataset_to_maf_dataset_wrapper(), tcga_datasets_to_data_pool(), user_data_filepath_to_class_maf_dataset_wrapper(), user_to_dataset_to_data_pool()

Examples

CRUX:::tcga_dataset_to_data_pool("ACC", CRUX:::new_maf_data_pool())

CCICB/CRUX documentation built on Jan. 28, 2024, 10:12 p.m.