AdjustedCopyEstimate {Repitools} | R Documentation

## 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.

[Package Repitools version 1.28.0 Index]