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.
TargetingMatrix 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.
If the input
mutabilityModel is of class
MutabilityModel, then the output
TargetingMatrix will carry over the input
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, c_call == "IGHA" & sample_id == "-1h") # Create 4x1024 models using only silent mutations sub_model <- createSubstitutionMatrix(db, model="s", sequenceColumn="sequence_alignment", germlineColumn="germline_alignment_d_mask", vCallColumn="v_call") mut_model <- createMutabilityMatrix(db, sub_model, model="s", sequenceColumn="sequence_alignment", germlineColumn="germline_alignment_d_mask", vCallColumn="v_call")
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)