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 |
calcDBExpectedMutations | Calculate expected mutation frequencies |
calcDBObservedMutations | Calculate observed numbers of mutations |
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 |
collapseByClone | Identifies clonal consensus 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 |
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 |
InfluenzaDb | Example Change-O database |
M1NDistance | Mouse single nucleotide distance matrix. |
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 |
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 |
summarizeBaseline | Calculate BASELINe summary statistics |
TargetingModel | S4 class defining a targeting model |
TargetingModel-class | S4 class defining a targeting model |
U5NModel | Uniform 5-mer targeting model. |
writeTargetingDistance | Write targeting model distances to a file |