Immunoglobulin Somatic Hypermutation Analysis

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Documentation for package ‘shazam’ version 1.2.0

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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