AdjustedCopyEstimate: 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.