shazam (version 0.1.2)

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 matrix 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.

Details

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

References

1. 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.

See Also

Other targeting model functions: calcTargetingDistance, createMutabilityMatrix, createSubstitutionMatrix, createTargetingModel, extendMutabilityMatrix, extendSubstitutionMatrix, plotMutability, writeTargetingDistance

Examples

# Subset example data to one isotype and sample as a demo
db <- subset(InfluenzaDb, CPRIMER == "IGHA" & BARCODE == "RL014")

# Create 4x1024 model using only silent mutations and ignore multiple mutations
sub_model <- createSubstitutionMatrix(db, model="S", multipleMutation="ignore")
mut_model <- createMutabilityMatrix(db, sub_model, model="S", multipleMutation="ignore",
                                    minNumSeqMutations=10)
tar_model <- createTargetingMatrix(sub_model, mut_model)

# Create 5x3125 model including Ns
sub_model <- extendSubstitutionMatrix(sub_model)
mut_model <- extendMutabilityMatrix(mut_model)
tar_model <- createTargetingMatrix(sub_model, mut_model)