createTargetingMatrix

createTargetingMatrix - Calculates a targeting rate matrix

Description¶

createTargetingMatrix calculates the targeting model matrix as the combined probability of mutability and substitution.

Usage¶

createTargetingMatrix(substitutionModel, mutabilityModel)

Arguments¶

substitutionModel: matrix of 5-mers substitution rates built by createSubstitutionMatrix or extendSubstitutionMatrix.
mutabilityModel: vector of 5-mers mutability rates built by createMutabilityMatrix or extendMutabilityMatrix.

Value¶

A TargetingMatrix with the same dimensions as the input substitutionModel 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 numMutS and numMutR slots.

Details¶

Targeting rates are calculated by multiplying the normalized mutability rate by the normalized substitution rates for each individual 5-mer.

References¶

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.

Examples¶

# Subset example data to 50 sequences, of one isotype and sample as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, c_call == "IGHA" & sample_id == "-1h")[1:50,]

# 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)