shazam (version 0.1.2)

extendSubstitutionMatrix: Extends a substitution model to include Ns.

Description

extendSubstitutionMatrix extends a 5-mer nucleotide substitution model with 5-mers that include Ns by averaging over all corresponding 5-mers without Ns.

Usage

extendSubstitutionMatrix(substitutionModel)

Arguments

substitutionModel

matrix of 5-mers substitution counts built by createSubstitutionMatrix.

Value

A 5x3125 matrix of normalized substitution rate for each 5-mer motif with rows names defining the center nucleotide, one of c("A", "C", "G", "T", "N"), and column names defining the 5-mer nucleotide sequence.

See Also

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

Examples

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

# Create model using only silent mutations and ignore multiple mutations
sub_model <- createSubstitutionMatrix(db, model="S", multipleMutation="ignore")
ext_model <- extendSubstitutionMatrix(sub_model)