TargetingModel-class - 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.

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.

See also

See createTargetingModel building models from sequencing data.