Calculates various call statistics per chromosome.
# S3 method for CBS
getCallStatistics(fit, regions=NULL, shrinkRegions=TRUE, ..., verbose=FALSE)Returns a CxK data.frame, where C is the number of regions that
meet the criteria setup by argument regions
and (K-4)/2 is the number of call types. The first column is the chromosome index, the second and the third are the first and last position, and the fourth the length (=last-first+1) of the chromosome. The following columns contains call summaries per chromosome. For each chromosome and call type, the total length of such calls on that chromosome is reported together how large of a fraction of the chromosome such calls occupy.
An optional data.frame with columns "chromosome",
"start", and "end" specifying the regions of interest to calculate
statistics for. If NULL, all of the genome is used.
If TRUE, regions are shrunk to the support of
the data.
Not used.
Verbose.
Henrik Bengtsson
The estimators implemented here are based solely on the segmentation results, which is very fast. In the original proposal by Fridlyand et al. [1], the authors estimates the parameters by converting segment-level calls back to locus-level calls and there do the calculations. The difference between the two approaches should be minor, particularly for large density arrays.
[1] Fridlyand et al. Breast tumor copy number aberration
phenotypes and genomic instability, BMC Cancer, 2006.
For more information see CBS.