somatic.CNV.call: Call somatic variants between healthy and disease tissues.

In drramki-chop/edm: Scalable workflow to identify copy Number variants from exome sequencing data

Description

Use read depth data from targeted sequencing experiments to call CNV between a tumor and matched healthy tissue.

Usage

somatic.CNV.call(normal, tumor, prop.tumor = 1, chromosome, start, end, names)

Arguments

normal	Read count data (numeric vector) for the normal tissue.
tumor	Read count data (numeric vector) for the tumor.
prop.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	Chromosome information for the bins.
start	Start position of each bin (typically in bp).
end	End position of each bin.
names	Names for each bin (tyically exon names but any way to track the bins will do).

Details

Experimental function at this stage.

Value

An ExomeDepth object with CNV calls.

Note

Absolutely experimental, not the main function from the package.

Author(s)

V. Plagnol

References

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling, Bioinformatics, In Press

drramki-chop/edm documentation built on June 6, 2020, 8:48 a.m.