ArrayViews-class        ArrayViews class, constructor, and methods
CopyNumScanParams-class
                        Parameters for parsing source files containing
                        SNP-array processed data, such as GenomeStudio
                        files for the Illumina platform
FilterParam-class       Container for the common criteria used to
                        filtering genomic ranges
HMM-class               Container for the segmented data and the
                        6-state HMM model parameters
HMMList                 Constructor for 'HMMList' class
HMMList-class           Class, constructor, and methods for
                        representing HMM results from multiple samples
HmmParam                Constructor for HmmParam class
HmmTrellisParam         Constructor for HmmTrellisParam class
IdiogramParams          Constructor for IdiogramParam objects
IdiogramParams-class    Paramater class for plotting idiograms
LogLik                  Constructor for LogLik class
LogLik-class            Classes and methods for storing/getting
                        log-likelihoods from Viterbi algorithm
NA_filter               Remove SNPs with NAs in any of the low-level
                        estimates
SnpArrayExperiment-class
                        A RangedSummarizedExperiment-derived class of
                        marker-level SNP array data for copy number
                        inference
SnpExperiment           Constructor for SnpArrayExperiment
SnpGRanges-class        An extension to GRanges for representing SNPs
TransitionParam         Constructor for TransitionParam class
VanillaICE              A hidden markov model for detection of germline
                        copy number variants from arrays
acf2                    Calculate lag10 autocorrelation
baumWelchUpdate         Function for updating parameters for emission
                        probabilities
calculateEmission       Calculate the emission probabilities for the
                        6-state HMM
cn_means                A parameter class for computing Emission
                        probabilities
cnvFilter               Filter the HMM-derived genomic ranges for copy
                        number variants
doUpdate                Helper function to determine whether to update
                        the HMM parameters via the Baum-Welch algorithm
dropDuplicatedMapLocs   Drop markers on the same chromosome having the
                        same genomic coordinates
dropSexChrom            Filter sex chromosomes
emission                Methods to set and get emission probabilities
emissionParam           Accessor for parameters used to compute
                        emission probabilities
filters                 Accessor for HMM filter parameters
genotypes               Accessor for SNP genotypes
getExampleSnpExperiment
                        Create an example SnpArrayExperiment from
                        source files containing marker-level genomic
                        data that are provided in this package
getHmmParams            Accessor for HMM model parameters
hmm2                    Fit a 6-state HMM to log R ratios and B allele
                        frequencies estimated from SNP arrays
hmmResults              Example output from the hidden markov model
isHeterozygous          Assess whether genotype is heterozygous based
                        on BAFs
lrrFile                 Accessors for objects of class ArrayViews
matrixOrNULL            A class allowing matrix or NULL objects
numberFeatures          The number of SNP/nonpolymorphic probes
                        contained in a genomic interval
parseSourceFile         Function for parsing GenomeStudio files
parsedPath              Complete path to directory for keeping parsed
                        files
probability             Accessor for probability filter
rescale                 Rescale a numeric vector
rowModes                Robust statistics for matrices
segs                    Accessor for the HMM segments
show,Viterbi-method     Show method for objects of class 'Viterbi'
snpArrayAssays          Create an assays object from log R ratios and B
                        allele frequencies
snp_exp                 An example SnpArrayExperiment
sourcePaths             Accessor for file paths containing SNP-level
                        summaries
start,oligoSnpSet-method
                        Retrieve genomic location of SNPs
state,HmmGRanges-method
                        Accessor for copy number state
state-methods           Accessor for the Viterbi state path
sweepMode               Sweep the modal log R ratio (by row or column)
                        from a matrix of log R ratios
threshold               Threshold numeric values
updateHmmParams         Run the Baum-Welch algorithm to update HMM
                        parameters
viewports               Default viewports for plotting CNV data with
                        lattice-style graphics
xyplotList              Lattice-style plots for granges and
                        SnpArrayExperiment objects
