Pedigree                Constructor for Pedigree class
Pedigree-class          Container for storing pedigree information
TrioSet                 Constructor for TrioSet objects.
TrioSet-class           Class '"TrioSet"'
TrioSetList             Constructs and object of class 'TrioSetList'
TrioSetList-class       Class '"TrioSetList"'
TrioSetListLD           Constructor for TrioSetList class for large
                        data
annotatedDataFrameFrom-methods
                        Methods for creating AnnotatedDataFrame objects
calculateMindist        Compute the minimum distance.
callDenovoSegments      Posterior calling for segmented data.
coerce,RangedDataCNV,GRanges-method
                        Methods for coercing objects from one class to
                        another
computeBayesFactor      Compute Bayes factors for minimum distance
                        segments
concAtTop               Functions for assessing concordance
correspondingCall       Find overlapping ranges
fatherPhenoData         Extract phenotype data for parents in a trio.
gcSubtract              Generic function for GC correction
isDenovo                Indicator for whether a trio copy number state
                        is a de novo copy number alteration.
mad2                    Methods for computing the minimum absolute
                        distance.
md.segs                 Objects containing segmented data
narrow                  Adjust breakpoints from segmentation inward
segment2                Wrapper for segment function in package DNAcopy
stackRangedDataList     Stack a list of RangedDataCBS objects.
trioSetListExample      An example of a 'TrioSetList' object
xypanelTrio             Panel function for a lattice-style plot of log
                        R ratios, BAFs, and the minimum distance for a
                        trio.
xyplotTrio              Function for plotting log R ratios, BAFs, and
                        the minimum distance for a trio using lattice.
