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.
exomeCopy