R: Copy number variant detection from exome sequencing read...
exomeCopy-package
R Documentation
Copy number variant detection from exome sequencing read depth
Description
Detection of copy number variants (CNV) from exome sequencing samples,
including unpaired samples. The package implements a hidden Markov
model which uses positional covariates, such as background read depth
and GC-content, to simultaneously normalize and segment the samples
into regions of constant copy count.
Details
exomeCopy fits a hidden Markov model to observed read counts using
covariates. It returns the Viterbi path, the most likely path of
hidden states, which is the predicted copy count at each window.
exomeCopy is designed to run on read counts from consecutive
genomic ranges on a single chromosome, as it tries to identify higher
or lower read depth relative to a baseline. Please see the vignette
for an example of how to prepare input data for exomeCopy, how
to loop the function over multiple chromosomes and samples, and how to
extract the resulting predicted CNVs.
References
Love, Michael I.; Mysickova, Alena; Sun, Ruping; Kalscheuer, Vera;
Vingron, Martin; and Haas, Stefan A. (2011) "Modeling Read Counts for
CNV Detection in Exome Sequencing Data," Statistical Applications in
Genetics and Molecular Biology: Vol. 10 : Iss. 1, Article 52. DOI: 10.2202/1544-6115.1732
http://cmb.molgen.mpg.de/publications/Love_2011_exomeCopy.pdf.