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.
Usage¶
"plot"(x, y, ...)
Arguments¶
- x
TargetingModelobject.- 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 occurring, 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 ofc("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.