DNAcopyParam            Constructor for DNAcopyParam class
FilterParamMD           Parameters for filtering results from the
                        segmentation and copy number inference
FilterParamMD-class     A class for filtering genomic intervals called
                        by MinimumDistance
MAP                     Computes the maximum a posteriori trio copy
                        number state for the segmented minimum distance
MAP2                    Computes maximum a posteriori estimate for the
                        trio copy number state
MDRanges-class          A 'GRanges'-derived class
MinDistExperiment       Constructor for 'MinDistExperiment' class
MinDistExperiment-class
                        Class and methods for MinDistExperiment
MinDistGRanges          Constructor for 'MinDistGRanges' class
MinDistGRanges-class    A container for storing segmentation data for
                        members in a 'ParentOffspring' family
MinDistParam            Constructor for 'MinDistParam' class
MinDistParam-class      Class and methods for parameters of minimum
                        distance algorithm
MinDistPosterior-class
                        Container for the segmentation results from a
                        MinDistExperiment
MinimumDistance         De novo copy number alterations in
                        parent-offspring trios
ParentOffspring-class   Object containing the sample identifiers for
                        members in a pedigree
ParentOffspringList-class
                        A list of 'ParentOffspring' objects
Pedigree                Deprecated function for constructing an
                        instance of class Pedigree
Pedigree-class          Deprecated class for storing pedigree data
PennParam               Constructor for class 'PennParam'
TrioSet                 Deprecated constructor for 'TrioSet' class
TrioSet-class           Deprecated class for storing low-level genomic
                        data for trios
TrioSetList             Constructor for 'TrioSetList' class
TrioSetList-class       Deprecated class for storing low-level genomic
                        data for trios
TrioSetListLD           Deprecated TrioSetList constructor for large
                        data
acf2                    Function for computing autocorrelations
calculateMindist        Deprecated function to calculate the minimum
                        distance
coerce                  Coercion methods in MinimumDistance package
denovoHemizygous        Filter the genomic intervals for denovo copy
                        number states
exampleTrioSetList      An example 'TrioSetList' object
filterExperiment        Methods for filtering MinDistExperiment objects
mad2                    Deprecated wrapper for computing the median
                        absolute deviation of low-level summaries
mdLegend                Text summary of information encapculated in a
                        MDRanges object for a particular interval
md_exp                  An example 'MinDistExperiment'
md_gr                   An example 'MinDistGRanges' object
mindist                 Getter and setter for the minimum distance
                        statistic
nMAD                    Setter and getter for number of median absolute
                        deviations the mean minimum distance of a
                        genomic interval is from zero
offspringNames          Deprecated functions and methods
pedigreeGrid            Plot the log R ratios and BAFs on a grid given
                        by precomputed viewports
pedigreeName            Accessor for pedigree name
pedigreeViewports       Default viewports for plotting log R ratios,
                        BAFs, chromosome idiogram, and a legend for a
                        case-parent trio
plotDenovo              Plot marker-level summaries for a genomic
                        interval of interest
range,ILimit-method     compute the range of an ILimit instance
segment2                A wrapper for DNAcopy's segment function
