createTargetingMatrix - Calculates a targeting rate matrix
createTargetingMatrix calculates the targeting model matrix as the
combined probability of mutability and substitution.
- matrix of 5-mers substitution rates built by createSubstitutionMatrix or extendSubstitutionMatrix.
- vector of 5-mers mutability rates built by createMutabilityMatrix or extendMutabilityMatrix.
A matrix with the same dimensions as the input
containing normalized targeting probabilities for each 5-mer motif with
row names defining the center nucleotide and column names defining the
5-mer nucleotide sequence.
Targeting rates are calculated by multiplying the normalized mutability rate by the normalized substitution rates for each individual 5-mer.
- Yaari G, et al. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013 4(November):358.
# Subset example data to one isotype and sample as a demo data(ExampleDb, package="alakazam") db <- subset(ExampleDb, ISOTYPE == "IgA" & SAMPLE == "-1h") # Create 4x1024 models using only silent mutations sub_model <- createSubstitutionMatrix(db, model="S") mut_model <- createMutabilityMatrix(db, sub_model, model="S")
Warning:Insufficient number of mutations to infer some 5-mers. Filled with 0.
# Extend substitution and mutability to including Ns (5x3125 model) sub_model <- extendSubstitutionMatrix(sub_model) mut_model <- extendMutabilityMatrix(mut_model) # Create targeting model from substitution and mutability tar_model <- createTargetingMatrix(sub_model, mut_model)