Function reference • gcap

Workflow Pipeline for implementing end-to-end analysis
`gcap.workflow()`	GCAP workflow for gene-level amplicon prediction
`gcap.workflow.seqz()`	GCAP sequenza workflow for gene-level amplicon prediction
`gcap.workflow.facets()`	GCAP FACETS workflow for gene-level amplicon prediction
`gcap.ASCNworkflow()`	GCAP workflow for gene-level amplicon prediction from ASCN input
`deploy()`	Deploy Command Line Interface to System Local Path
Class Package builtin class
`fCNA`	R6 class representing focal copy number amplification list predicted from a cohort
Analysis Wrapper Core build block for constructing pipeline
`gcap.runASCAT()`	Run ASCAT on tumor-normal pair WES data files
`gcap.runBuildflow()`	Build data for prediction from ASCAT result files
`gcap.runPrediction()`	Run gene-level circular prediction
`gcap.runScoring()`	Summarize prediction result into gene/sample-level
`gcap.runASCNBuildflow()`	Build data for prediction from absolute copy number data
Individual Analysis Modules Individual data processing and analysis functions
`gcap.extractFeatures()`	Extract sample and region level features
`gcap.collapse2Genes()`	Generate unified gene-level feature data
`get_auc()`	Get AUC value
`mergeDTs()`	Merge a list of data.table
`overlaps()`	Get overlaps of two genomic regions
Datasets Builtin datasets
`ec`	Example ecDNA training data
`ascn`	Example allele specific copy number (ASCN) data
`oncogenes`	Oncogene list

Reference