Container for results of GC adjusted copy number estimation.

Description

Contains the genomic coordinates of regions, the raw counts before GC adjustment, the GC content and mappability of each region, and the polynomial model fit, and the GC-adjusted copy number estimates.

Constructor

AdjustedCopyEstimate(ploidy, windows, mappability, gc, unadj.CN, models, adj.CN) Creates a AdjustedCopyEstimate object.

ploidy

Sets of chromosomes in each sample.

windows

A GRanges object.

mappability

A numeric vector of mappability. Elements between 0 and 1.

gc

A numeric vector of GC content Elements between 0 and 1.

unadj.CN

A matrix of estimated copy numbers after mappability adjustment, but before GC content adjustment, if slot type is "absolute". Otherwise, fold changes.

models

The polynomial models that were fit to the counts.

adj.CN

A matrix of estimated copy numbers after mappability adjustment and GC content adjustment, if slot type is "absolute". Otherwise, a matrix of fold changes, based on GC adjusted absolute copy estimates.

Note that mappability and gc become metadata columns of windows when the object is created.

Superclass

This class inherits from CopyEstimate.

Additional Slots

These are added to by absoluteCN or relativeCN

unadj.CN.seg

A GRangesList of copy number segmentations for each sample.

adj.CN.seg

A GRangesList of copy number segmentations for each sample, using GC adjusted data.

type

A flag that contains if the copy number data is absolute or relative.

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