# Immunoglobulin Somatic Hypermutation Analysis

## Documentation for package ‘shazam’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

as.data.frame-method | S4 class defining a mutability model
Baseline | S4 class defining a BASELINe (selection) object
Baseline-class | S4 class defining a BASELINe (selection) object
Baseline-method | S4 class defining a BASELINe (selection) object
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
CHARGE_MUTATIONS | Amino acid mutation definitions
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 | Output of the 'dens' method of findThreshold
DensityThreshold-class | Output of the 'dens' method of findThreshold
DensityThreshold-method | 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 | Output of the 'gmm' method of findThreshold
GmmThreshold-class | Output of the 'gmm' method of findThreshold
GmmThreshold-method | Output of the 'gmm' method of findThreshold
groupBaseline | Group BASELINe PDFs
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.
HYDROPATHY_MUTATIONS | Amino acid mutation definitions
IMGT_SCHEMES | IMGT unique numbering schemes
IMGT_V | IMGT unique numbering schemes
IMGT_VDJ | IMGT unique numbering schemes
IMGT_VDJ_BY_REGIONS | IMGT unique numbering schemes
IMGT_V_BY_CODONS | IMGT unique numbering schemes
IMGT_V_BY_REGIONS | IMGT unique numbering schemes
IMGT_V_BY_SEGMENTS | IMGT unique numbering schemes
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
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.
MutabilityModel | S4 class defining a mutability model
MutabilityModel-class | S4 class defining a mutability model
MutabilityModel-method | S4 class defining a mutability model
MutationDefinition | S4 class defining replacement and silent mutation definitions
MutationDefinition-class | S4 class defining replacement and silent mutation definitions
MUTATION_SCHEMES | Amino acid mutation definitions
observedMutations | Calculate observed numbers of mutations
plot-method | S4 class defining a BASELINe (selection) object
plot-method | Output of the 'dens' method of findThreshold
plot-method | Output of the 'gmm' method of findThreshold
plot-method | S4 class defining a targeting model
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
POLARITY_MUTATIONS | Amino acid mutation definitions
print-method | Output of the 'dens' method of findThreshold
print-method | Output of the 'gmm' method of findThreshold
print-method | S4 class defining a mutability model
RegionDefinition | S4 class defining a region definition
RegionDefinition-class | S4 class defining a region definition
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
summary-method | S4 class defining a BASELINe (selection) object
TargetingMatrix | S4 class defining a targeting matrix
TargetingMatrix-class | S4 class defining a targeting matrix
TargetingModel | S4 class defining a targeting model
TargetingModel-class | S4 class defining a targeting model
TargetingModel-method | S4 class defining a targeting model
testBaseline | Two-sided test of BASELINe PDFs
U5N | Uniform 5-mer null targeting model.
VOLUME_MUTATIONS | Amino acid mutation definitions
writeTargetingDistance | Write targeting model distances to a file