Restructuring_AbstractCBS_objects: Restructuring AbstractCBS objects

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Restructuring AbstractCBS objects

Description

This page describes available methods for restructuring an AbstractCBS object.

• *extractChromosomes() / *extractChromosome() - Extracts an AbstractCBS with the specified chromosomes.

• *extractSegments() / *extractSegment() - Extracts an AbstractCBS with the specified segments.

• *extractRegions() / *extractRegion() - Extracts an AbstractCBS with the specified regions each of a certain size, where a region is defined as a connected set of segments.

• *dropRegions() / *dropRegion() - Drops specified regions and returns an AbstractCBS without them.

• *dropChangePoint() / *mergeTwoSegments() - Drops a change point by merging two neighboring segments and recalculates the statistics for the merged segment before returning an AbstractCBS.

• *dropChangePoints() - Drops zero or more change points and recalculates the segment statistics before returning an AbstractCBS.

• *mergeThreeSegments() - Merges a segment with its two flanking segments and recalculates the statistics for the merged segment before returning an AbstractCBS.

All of the above methods are implemented for CBS and PairedPSCBS objects.

Author(s)

Henrik Bengtsson

See Also

For more information see AbstractCBS.

HenrikBengtsson/PSCBS documentation built on June 8, 2025, 10:40 p.m.