CountOverlaps method from IRanges Package

countOverlaps is a method from the IRanges package in Bioconductor which counts interval overlaps between two "range-based" objects: a query and a subject. ‘countOverlaps’ returns the overlap hit count for each range in ‘query’ using the specified parameters which can be looked up using ?countOverlaps in a R session.

We can use the countOverlaps function to conduct a copy Number analysis for a pair of tumor sample/normal sample bam files.

We employed this approach to our sample Dataset and the plots generated are shown below. ![] (https://raw.github.com/Bioconductor/copy-number-analysis/master/image/cnv-countOverlaps.png)

The counts for tumor and normal sample can be viewed at : countOverlapresults.tsv

The R code for this analysis can be found at: cnv-countOverlaps.R