TargetingModel defines a common data structure for mutability, substitution and
targeting of immunoglobulin (Ig) sequencing data in a 5-mer microsequence context.
# S4 method for TargetingModel,missing
plot(x, y, ...)TargetingModel object.
ignored.
arguments to pass to plotMutability.
nameName of the model.
descriptionDescription of the model and its source data.
speciesGenus and species of the source sequencing data.
dateDate the model was built.
citationPublication source.
substitutionNormalized rates of the center nucleotide of a given 5-mer
mutating to a different nucleotide. The substitution model
is stored as a 5x3125 matrix of rates. Rows define
the mutated nucleotide at the center of each 5-mer, one of
c("A", "C", "G", "T", "N"), and columns define the
complete 5-mer of the unmutated nucleotide sequence.
mutabilityNormalized rates of a given 5-mer being mutated. The mutability model is stored as a numeric vector of length 3125 with mutability rates for each 5-mer. Note that "normalized" means that the mutability rates for the 1024 5-mers that contain no "N" at any position sums up to 1 (as opposed to the entire vector summing up to 1).
targetingRate matrix of a given mutation ocurring, defined as
\(mutability * substitution\). The targeting model
is stored as a 5x3125 matrix. Rows define
the mutated nucleotide at the center of each 5-mer, one of
c("A", "C", "G", "T", "N"), and columns define the complete 5-mer
of the unmutated nucleotide sequence.
numMutSnumber indicating the number of silent mutations used for estimating mutability.
numMutRnumber indicating the number of replacement mutations used for estimating mutability.
See createTargetingModel building models from sequencing data.