Container for results of GC adjusted copy number estimation.
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.
AdjustedCopyEstimate(ploidy, windows, mappability, gc, unadj.CN, models, adj.CN)Creates a AdjustedCopyEstimate object.
Sets of chromosomes in each sample.
A numeric vector of mappability. Elements between 0 and 1.
A numeric vector of GC content Elements between 0 and 1.
A matrix of estimated copy numbers after mappability adjustment, but before GC content adjustment, if slot
"absolute". Otherwise, fold changes.
The polynomial models that were fit to the counts.
A matrix of estimated copy numbers after mappability adjustment and GC content adjustment, if slot
"absolute". Otherwise, a matrix of fold changes, based on GC adjusted absolute copy estimates.
gc become metadata columns of
when the object is created.
This class inherits from
These are added to by
GRangesListof copy number segmentations for each sample.
GRangesListof copy number segmentations for each sample, using GC adjusted data.
A flag that contains if the copy number data is absolute or relative.