Immunoglobulin Somatic Hypermutation Analysis


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Documentation for package ‘shazam’ version 0.1.4

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shazam-package The shazam package
Baseline S4 class defining a BASELINe (selection) object
Baseline-class S4 class defining a BASELINe (selection) object
calcBaseline Calculate the BASELINe PDFs
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
CHARGE_MUTATIONS Amino acid mutation definitions
clearConsole Clears the console
collapseClones Constructs effective clonal sequences
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
expectedMutations Calculate expected mutation frequencies
extendMutabilityMatrix Extends a mutability model to include Ns.
extendSubstitutionMatrix Extends a substitution model to include Ns.
getBaselineStats Gets the summary statistics of a Baseline object
getnproc Determines the numbers of CPU cores available
getPlatform Determines the OS platform being used
groupBaseline Group BASELINe PDFs
HS1FDistance Human single nucleotide distance matrix.
HS5FModel Human 5-mer targeting model.
HYDROPATHY_MUTATIONS Amino acid mutation definitions
IMGT_SCHEMES IMGT unique numbering schemes
IMGT_V IMGT unique numbering schemes
IMGT_V_BY_REGIONS IMGT unique numbering schemes
IMGT_V_BY_REGIONS_NO_CDR3 IMGT unique numbering schemes
IMGT_V_NO_CDR3 IMGT unique numbering schemes
M1NDistance Mouse single nucleotide distance matrix.
MRS5NFModel Mouse 5-mer targeting 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
plotBaselineDensity Plots BASELINe probability density functions
plotBaselineSummary Plots BASELINe summary statistics
plotMutability Plot mutability probabilities
POLARITY_MUTATIONS Amino acid mutation definitions
RegionDefinition S4 class defining a region definition
RegionDefinition-class S4 class defining a region definition
shazam The shazam package
shmulateSeq Simulate mutations in a single sequence
shmulateTree Simulate mutations in a lineage tree
summarizeBaseline Calculate BASELINe summary statistics
TargetingModel S4 class defining a targeting model
TargetingModel-class S4 class defining a targeting model
testBaseline Two-sided test of BASELINe PDFs
U5NModel Uniform 5-mer targeting model.
VOLUME_MUTATIONS Amino acid mutation definitions
writeTargetingDistance Write targeting model distances to a file