| Baseline-class | S4 class defining a BASELINe (selection) object |
| calcBaseline | Calculate the BASELINe PDFs (including for regions that... |
| 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... |
| 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 |
| DensityThreshold-class | Output of the 'dens' method of findThreshold |
| 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 |
| GmmThreshold-class | Output of the 'gmm' method of findThreshold |
| groupBaseline | Group BASELINe PDFs |
| HH_S1F | Human heavy chain, silent, 1-mer, functional substitution... |
| HH_S5F | Human heavy chain, silent, 5-mer, functional targeting model. |
| HKL_S1F | Human kappa and lambda chain, silent, 1-mer, functional... |
| HKL_S5F | Human kappa and lambda light chain, silent, 5-mer, functional... |
| IMGT_SCHEMES | IMGT unique numbering schemes |
| makeAverage1merMut | Make a 1-mer mutability model by averaging over a 5-mer... |
| makeAverage1merSub | Make a 1-mer substitution model by averaging over a 5-mer... |
| makeDegenerate5merMut | Make a degenerate 5-mer mutability model based on a 1-mer... |
| makeDegenerate5merSub | Make a degenerate 5-mer substitution model based on a 1-mer... |
| makeGraphDf | Build a data.frame from a ChangeoClone and an igraph object... |
| minNumMutationsTune | Parameter tuning for minNumMutations |
| minNumSeqMutationsTune | Parameter tuning for minNumSeqMutations |
| MK_RS1NF | Mouse kappa chain, replacement and silent, 1-mer,... |
| MK_RS5NF | Mouse kappa light chain, replacement and silent, 5-mer,... |
| MutabilityModel-class | S4 class defining a mutability model |
| MutationDefinition-class | S4 class defining replacement and silent mutation definitions |
| MUTATION_SCHEMES | Amino acid mutation definitions |
| 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... |
| RegionDefinition-class | S4 class defining a region definition |
| setRegionBoundaries | Build a RegionDefinition object that includes CDR3 and FWR4. |
| shazam | The shazam package |
| shazam-package | shazam: Immunoglobulin Somatic Hypermutation Analysis |
| shmulateSeq | Simulate mutations in a single sequence |
| shmulateTree | Simulate mutations in a lineage tree |
| slideWindowDb | Sliding window approach towards filtering sequences in a... |
| slideWindowSeq | Sliding window approach towards filtering a single sequence |
| slideWindowTune | Parameter tuning for sliding window approach |
| slideWindowTunePlot | slideWindowTunePlot - plotSlideWindowTune backward... |
| summarizeBaseline | Calculate BASELINe summary statistics |
| TargetingMatrix-class | S4 class defining a targeting matrix |
| TargetingModel-class | S4 class defining a targeting model |
| testBaseline | Two-sided test of BASELINe PDFs |
| U5N | Uniform 5-mer null targeting model. |
| writeTargetingDistance | Write targeting model distances to a file |
