TargetingModel-class {shazam}

S4 class defining a targeting model

Description

TargetingModel defines a common data structure for mutability, substitution and targeting of immunoglobulin (Ig) sequencing data in a 5-mer microsequence context.

Usage

## S4 method for signature 'TargetingModel,missing'
plot(x, y, ...)

Arguments

x

TargetingModel object.

y

ignored.

...

arguments to pass to plotMutability.

Slots

name

Name of the model.

description

Description of the model and its source data.

species

Genus and species of the source sequencing data.

date

Date the model was built.

citation

Publication source.

substitution

Normalized 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.

mutability

Normalized 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).

targeting

Rate 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.

numMutS

number indicating the number of silent mutations used for estimating mutability.

numMutR

number indicating the number of replacement mutations used for estimating mutability.

See Also

See createTargetingModel building models from sequencing data.