Man pages for shazam
Immunoglobulin Somatic Hypermutation Analysis

Baseline-classS4 class defining a BASELINe (selection) object
calcBaselineCalculate the BASELINe PDFs
calcExpectedMutationsCalculate expected mutation frequencies of a sequence
calcObservedMutationsCount the number of observed mutations in a sequence.
calcTargetingDistanceCalculates a 5-mer distance matrix from a TargetingModel...
calculateMutabilityCalculate total mutability
clearConsoleClears the console
collapseClonesConstructs effective clonal sequences for all clones
createBaselineCreates a Baseline object
createMutabilityMatrixBuilds a mutability model
createMutationDefinitionCreates a MutationDefinition
createRegionDefinitionCreates a RegionDefinition
createSubstitutionMatrixBuilds a substitution model
createTargetingMatrixCalculates a targeting rate matrix
createTargetingModelCreates a TargetingModel
DensityThreshold-classOutput of the 'dens' method of findThreshold
distToNearestDistance to nearest neighbor
editBaselineEdit the Baseline object
expectedMutationsCalculate expected mutation frequencies
extendMutabilityMatrixExtends a mutability model to include Ns.
extendSubstitutionMatrixExtends a substitution model to include Ns.
findThresholdFind distance threshold
getnprocDetermines the numbers of CPU cores available
getPlatformDetermines the OS platform being used
GmmThreshold-classOutput of the 'gmm' method of findThreshold
groupBaselineGroup BASELINe PDFs
HH_S1FHuman heavy chain, silent, 1-mer, functional substitution...
HH_S5FHuman heavy chain, silent, 5-mer, functional targeting model.
HKL_S1FHuman kappa and lambda chain, silent, 1-mer, functional...
HKL_S5FHuman kappa and lambda light chain, silent, 5-mer, functional...
IMGT_SCHEMESIMGT unique numbering schemes
makeAverage1merMutMake a 1-mer mutability model by averaging over a 5-mer...
makeAverage1merSubMake a 1-mer substitution model by averaging over a 5-mer...
makeDegenerate5merMutMake a degenerate 5-mer mutability model based on a 1-mer...
makeDegenerate5merSubMake a degenerate 5-mer substitution model based on a 1-mer...
minNumMutationsTuneParameter tuning for minNumMutations
minNumSeqMutationsTuneParameter tuning for minNumSeqMutations
MK_RS1NFMouse kappa chain, replacement and silent, 1-mer,...
MK_RS5NFMouse kappa light chain, replacement and silent, 5-mer,...
MutationDefinition-classS4 class defining replacement and silent mutation definitions
MUTATION_SCHEMESAmino acid mutation definitions
observedMutationsCalculate observed numbers of mutations
plotBaselineDensityPlots BASELINe probability density functions
plotBaselineSummaryPlots BASELINe summary statistics
plotDensityThresholdPlot findThreshold results for the density method
plotGmmThresholdPlot findThreshold results for the gmm method
plotMutabilityPlot mutability probabilities
plotTuneVisualize parameter tuning for minNumMutations and...
RegionDefinition-classS4 class defining a region definition
shazamThe shazam package
shmulateSeqSimulate mutations in a single sequence
shmulateTreeSimulate mutations in a lineage tree
slideWindowDbSliding window approach towards filtering sequences in a...
slideWindowSeqSliding window approach towards filtering a single sequence
slideWindowTuneParameter tuning for sliding window approach
slideWindowTunePlotVisualize parameter tuning for sliding window approach
summarizeBaselineCalculate BASELINe summary statistics
TargetingModel-classS4 class defining a targeting model
testBaselineTwo-sided test of BASELINe PDFs
U5NUniform 5-mer null targeting model.
writeTargetingDistanceWrite targeting model distances to a file
shazam documentation built on April 1, 2018, 12:01 p.m.