Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

Description

Perform joint segmentation on two signal dimensions derived from total read depth (intensity) and allele specific read depth (intensity) for whole genome sequencing (WGS), whole exome sequencing (WES) and SNP array data.

Details

See the vignettes of the package for more details.

Author(s)

Zhongyang Zhang [aut, cre], Ke Hao [aut], Nancy R. Zhang [ctb]

Maintainer: Zhongyang Zhang <zhongyang.zhang@mssm.edu>

References

Zhang, Z. and Hao, K. (2015) SAAS-CNV: A joint segmentation approach on aggregated and allele specific signals for the identification of somatic copy number alterations with next-generation sequencing Data. PLoS Computational Biology, 11(11):e1004618.

Zhang, N. R., Siegmund, D. O., Ji, H., Li, J. Z. (2010) Detecting simultaneous changepoints in multiple sequences. Biometrika, 97(3):631–645.

See Also

DNAcopy

Examples

## See the vignettes of the package for examples.

Results