Use read depth data from targeted sequencing experiments to call CNV between a tumor and matched healthy tissue.
somatic.CNV.call(normal, tumor, prop.tumor = 1, chromosome, start, end, names)Read count data (numeric vector) for the normal tissue.
Read count data (numeric vector) for the tumor.
Proportion of the tumour DNA in the tumour sample (between 0 and 1, and less than 1 if there is normal tissue in the tumor sample).
Chromosome information for the bins.
Start position of each bin (typically in bp).
End position of each bin.
Names for each bin (tyically exon names but any way to track the bins will do).
An ExomeDepth object with CNV calls.
Experimental function at this stage.
A robust model for read count data in exome sequencing experiments and implications for copy number variant calling, Bioinformatics, In Press