cnvlib.rst

Python API (cnvlib package)

Module cnvlib contents

cnvlib

The one function exposed at the top level, read, loads a file in CNVkit's native format and returns a CopyNumArray instance. For your own scripting, you can usually accomplish what you need using the CopyNumArray and GenomicArray methods available on this returned object.

Core classes

The core objects used throughout CNVkit. The base class is GenomicArray. All of these classes wrap a pandas DataFrame instance accessible through the .data attribute which can be used for any manipulations that aren't already provided by methods in the wrapper class.

gary

cnvlib.gary

cnary

cnvlib.cnary

rary

cnvlib.rary

vary

cnvlib.vary

Interface to CNVkit sub-commands

commands

The public API for each of the commands defined in the CNVkit workflow.

cnvlib.commands

The following modules implement lower-level functionality specific to each of the CNVkit sub-commands.

antitarget

cnvlib.antitarget

call

cnvlib.call

coverage

cnvlib.coverage

diagram

cnvlib.diagram

export

cnvlib.export

fix

cnvlib.fix

importers

cnvlib.importers

reference

cnvlib.reference

reports

Supports the sub-commands breaks and gainloss.

cnvlib.reports

segmentation

cnvlib.segmentation

target

cnvlib.target

Helper modules

core

cnvlib.core

metrics

cnvlib.metrics

ngfrills

cnvlib.ngfrills

parallel

cnvlib.parallel

params

Defines several constants used in the pipeline.

cnvlib.params

plots

cnvlib.plots

smoothing

cnvlib.smoothing