Fit the exomeCopy or exomeCopyVar model to the observed counts.
Description
Fits a hidden Markov model to observed read counts using positional covariates. It returns an object containing the fitted parameters and 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
requires as input a RangedData
object
containing read counts in genomic ranges along with the covariates.
Some convenience functions are provided for preparing input for
exomeCopy
:

subdivideGRanges
, to subdivide aGRanges
object containing the genomic ranges of the targeted region into genomic ranges of nearly equal width, 
countBamInGRanges
, to count the number of read starts from a BAM read mapping file in aGRanges
object, 
getGCcontent
, to get the GCcontent in the ranges given a FASTA file of the reference sequence, 
generateBackground
, to calculate median normalized read depth over a set of control samples, and also any statistic over normalized read depth.
Usage
1 2 3  exomeCopy(rdata, sample.name, X.names, Y.names, fit.var=FALSE, reltol
= 0.0001, S = 0:4, d = 2, goto.cnv = 1e4, goto.normal = 1/20,
init.phi="norm")

Arguments
rdata 
A RangedData object with the sample counts and positional covariates over the genomic ranges. 
sample.name 
The name of the value column of rdata with the sample read counts. 
X.names 
The names of the value columns of rdata with covariates for estimating mu. 
Y.names 
(optional) the names of the value columns of rdata with covariates for estimating phi, only required if fit.var = TRUE. 
fit.var 
A logical, whether the model should fit the overdispersion parameter phi with a linear combination of covariates (exomeCopyVar) or with a scalar (exomeCopy). Defaults to FALSE (exomeCopy). 
reltol 
The relative tolerance for convergence used in the 
S 
A vector of possible copy numbers for the different states. 
d 
The expected copy number for the normal state. This should be set to 2 for autosomes and 1 for haploid data. 
goto.cnv 
The initial setting for probability to transfer to a CNV state. 
goto.normal 
The initial setting for probability to transfer to a normal state. 
init.phi 
Either "norm" or "counts": initialize phi with the moment estimate using residuals from a linear model of read counts on covariates or with the raw counts. 
Details
exomeCopy
fits transitional and emission parameters of an HMM to best
explain the observed counts of a sample from exome or targeted
sequencing. The set of underlying copy number states, S, in the
sample must be provided before running the algorithm.
The emission probabilities are given as a negative binomial
distribution using positional covariates, such as log background read
depth, quadratic terms for GCcontent, and range width, which are
stored in a matrix X. Optionally, for fitting the variance of the
distribution, the standard deviation and/or variance of the background
set can be included in a matrix Y. All covariates are normalized
within exomeCopy
for improved optimization.
For the observed count at range t, O_t, the emission probability is given by:
O_t ~ NB(mu_ti, phi)
The mean parameter mu_ti is given by:
mu_ti = (S_i / d) e^(x_t* beta)
Here S_i is the ith possible copy number state, d is the expected background copy number (d = 2 for diploid sequence), and beta is a vector of coefficients fitted by the model. x_t* is the tth row of the matrix X.
mu must be positive, so it is replaced with a small positive number if the value is less than zero.
For exomeCopyVar, which also fits the variance, the emission probability includes a locationdependent dispersion parameter.
where
log(phi_t) = y_t* gamma
or a small positive number if this is less than zero.
Two transition probabilities are fitted in the model: the probabilities of transitioning to a normal state and to a CNV state.
exomeCopy
calls negLogLike
to evaluate the likelihood of
the HMM. The parameters are fit using NelderMead optimization with
the optim
function on the negative likelihood. The
Viterbi path is calculated by calling viterbiPath
.
Value
Returns an ExomeCopyclass
object. See this page for the
slot descriptions. Also see the vignette and
copyCountSegments
on how to extract segments.
Author(s)
Michael Love
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: 10.2202/15446115.1732 http://cmb.molgen.mpg.de/publications/Love_2011_exomeCopy.pdf.
References for HMM algorithms and use of HMM for segmentation of genomic data by copy number:
Rabiner, L. R. (1989): "A tutorial on hidden Markov models and selected applications in speech recognition," Proceedings of the IEEE, 77, 257, 286, http://dx.doi.org/10.1109/5.18626.
Fridlyand, J., A. M. Snijders, D. Pinkel, D. G. Albertson, and Jain (2004): "Hidden Markov models approach to the analysis of array CGH data," Journal of Multivariate Analysis, 90, 132, 153, http://dx.doi.org/10.1016/j.jmva.2004.02.008.
Marioni, J. C., N. P. Thorne, and S. Tavare (2006):"BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data." Bioinformatics, 22, 1144, 1146, http://view.ncbi.nlm.nih.gov/pubmed/16533818.
See Also
ExomeCopyclass
subdivideGRanges
countBamInGRanges
copyCountSegments
plot.ExomeCopy
negLogLike
IRanges
RangedData
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40  ## The following is an example of running exomeCopy on simulated
## read counts using the model parameters defined above. For an example
## using real exome sequencing read counts (with simulated CNV) please
## see the vignette.
## create RangedData for storing genomic ranges and covariate data
## (background, background stdev, GCcontent)
m < 5000
rdata < RangedData(IRanges(start=0:(m1)*100+1,width=100),
space=rep("chr1",m), universe="hg19", log.bg=rnorm(m), log.bg.var=rnorm(m),
gc=runif(m,30,50))
## create read depth distributional parameters mu and phi
rdata$gc.sq < rdata$gc^2
X < cbind(bg=rdata$log.bg,gc=rdata$gc,gc.sq=rdata$gc.sq)
Y < cbind(bg.sd=rdata$log.bg.var)
beta < c(5,1,.01,.01)
gamma < c(3,.1)
rdata$mu < exp(beta[1] + scale(X) %*% beta[2:4])
rdata$phi < exp(gamma[1] + scale(Y) %*% gamma[2])
## create observed counts with simulated heterozygous duplication
cnv.nranges < 200
bounds < (round(m/2)+1):(round(m/2)+cnv.nranges)
O < rnbinom(nrow(rdata),mu=rdata$mu,size=1/rdata$phi)
O[bounds] < O[bounds] + rbinom(cnv.nranges,prob=0.5,size=O[bounds])
rdata[["sample1"]] < O
## run exomeCopy() and list segments
fit < exomeCopy(rdata,"sample1",X.names=c("log.bg","gc","gc.sq"))
# an example call with variance fitting.
# see paper: this does not necessarily improve the fit
fit < exomeCopy(rdata,"sample1",X.names=c("log.bg","gc","gc.sq"),
Y.names="log.bg",fit.var=TRUE)
## see man page for copyCountSegments() for summary of
## the predicted segments of constant copy count, and
## for plot.ExomeCopy() for plotting fitted objects

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