getCallStatistics.CBS: Calculates various call statistics per chromosome
Description
Calculates various call statistics per chromosome.Usage
## S3 method for class 'CBS':
getCallStatistics(fit, regions=NULL, shrinkRegions=TRUE, ..., verbose=FALSE)
Arguments
regions
An optional data.frame with columns "chromosome",
"start", and "end" specifying the regions of interest to calculate
statistics for. If NULL shrinkRegions
If TRUE, regions are shrunk to the support of
the data. Value
- 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.
Details
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.References
[1] Fridlyand et al. Breast tumor copy number aberration
phenotypes and genomic instability, BMC Cancer, 2006.See Also
For more information see CBS.