getCallStatistics.CBS: Calculates various call statistics per chromosome

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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, all of the genome is used.
shrinkRegions	If TRUE, regions are shrunk to the support of the data.
...	Not used.
verbose	Verbose.

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.

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.

Author(s)

Henrik Bengtsson

References

[1] Fridlyand et al. Breast tumor copy number aberration phenotypes and genomic instability, BMC Cancer, 2006.

See Also

For more information see CBS.

PSCBS documentation built on Oct. 23, 2021, 9:09 a.m.