Call somatic variants between healthy and disease tissues.

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Description

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

Usage

1
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

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