Baseline-class          S4 class defining a BASELINe (selection) object
DensityThreshold-class
                        Output of the 'dens' method of findThreshold
GmmThreshold-class      Output of the 'gmm' method of findThreshold
HH_S1F                  Human heavy chain, silent, 1-mer, functional
                        substitution model.
HH_S5F                  Human heavy chain, silent, 5-mer, functional
                        targeting model.
HKL_S1F                 Human kappa and lambda chain, silent, 1-mer,
                        functional substitution model.
HKL_S5F                 Human kappa and lambda light chain, silent,
                        5-mer, functional targeting model.
IMGT_SCHEMES            IMGT unique numbering schemes
MK_RS1NF                Mouse kappa chain, replacement and silent,
                        1-mer, non-functional substitution model.
MK_RS5NF                Mouse kappa light chain, replacement and
                        silent, 5-mer, non-functional targeting model.
MUTATION_SCHEMES        Amino acid mutation definitions
MutabilityModel-class   S4 class defining a mutability model
MutationDefinition-class
                        S4 class defining replacement and silent
                        mutation definitions
RegionDefinition-class
                        S4 class defining a region definition
TargetingMatrix-class   S4 class defining a targeting matrix
TargetingModel-class    S4 class defining a targeting model
U5N                     Uniform 5-mer null targeting model.
calcBaseline            Calculate the BASELINe PDFs (including for
                        regions that include CDR3 and FWR4)
calcExpectedMutations   Calculate expected mutation frequencies of a
                        sequence
calcObservedMutations   Count the number of observed mutations in a
                        sequence.
calcTargetingDistance   Calculates a 5-mer distance matrix from a
                        TargetingModel object
calculateMutability     Calculate total mutability
collapseClones          Constructs effective clonal sequences for all
                        clones
consensusSequence       Construct a consensus sequence
convertNumbering        convertNumbering: IMGT-Kabat number conversion
createBaseline          Creates a Baseline object
createMutabilityMatrix
                        Builds a mutability model
createMutationDefinition
                        Creates a MutationDefinition
createRegionDefinition
                        Creates a RegionDefinition
createSubstitutionMatrix
                        Builds a substitution model
createTargetingMatrix   Calculates a targeting rate matrix
createTargetingModel    Creates a TargetingModel
distToNearest           Distance to nearest neighbor
editBaseline            Edit the Baseline object
expectedMutations       Calculate expected mutation frequencies
extendMutabilityMatrix
                        Extends a mutability model to include Ns.
extendSubstitutionMatrix
                        Extends a substitution model to include Ns.
findThreshold           Find distance threshold
groupBaseline           Group BASELINe PDFs
makeAverage1merMut      Make a 1-mer mutability model by averaging over
                        a 5-mer mutability model
makeAverage1merSub      Make a 1-mer substitution model by averaging
                        over a 5-mer substitution model
makeDegenerate5merMut   Make a degenerate 5-mer mutability model based
                        on a 1-mer mutability model
makeDegenerate5merSub   Make a degenerate 5-mer substitution model
                        based on a 1-mer substitution model
makeGraphDf             Build a data.frame from a ChangeoClone and an
                        igraph object containing a clonal lineage
minNumMutationsTune     Parameter tuning for minNumMutations
minNumSeqMutationsTune
                        Parameter tuning for minNumSeqMutations
observedMutations       Calculate observed numbers of mutations
plotBaselineDensity     Plots BASELINe probability density functions
plotBaselineSummary     Plots BASELINe summary statistics
plotDensityThreshold    Plot findThreshold results for the density
                        method
plotGmmThreshold        Plot findThreshold results for the gmm method
plotMutability          Plot mutability probabilities
plotSlideWindowTune     Visualize parameter tuning for sliding window
                        approach
plotTune                Visualize parameter tuning for minNumMutations
                        and minNumSeqMutations
setRegionBoundaries     Build a RegionDefinition object that includes
                        CDR3 and FWR4.
shazam                  The shazam package
shmulateSeq             Simulate mutations in a single sequence
shmulateTree            Simulate mutations in a lineage tree
slideWindowDb           Sliding window approach towards filtering
                        sequences in a 'data.frame'
slideWindowSeq          Sliding window approach towards filtering a
                        single sequence
slideWindowTune         Parameter tuning for sliding window approach
slideWindowTunePlot     slideWindowTunePlot - plotSlideWindowTune
                        backward compatability
summarizeBaseline       Calculate BASELINe summary statistics
testBaseline            Two-sided test of BASELINe PDFs
writeTargetingDistance
                        Write targeting model distances to a file
