shazam (version 0.1.9)

extendMutabilityMatrix: Extends a mutability model to include Ns.

Description

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

Usage

extendMutabilityMatrix(mutabilityModel)

Arguments

mutabilityModel

vector of 5-mer mutability rates built by createMutabilityMatrix.

Value

A 3125 vector of normalized mutability rates for each 5-mer motif with names defining the 5-mer nucleotide sequence. Note that "normalized" means that the mutability rates for the 1024 5-mers that contain no "N" at any position sums up to 1 (as opposed to the entire vector summing up to 1).

See Also

createMutabilityMatrix, extendSubstitutionMatrix

Examples

# NOT RUN {
# Subset example data to one isotype and sample as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, ISOTYPE == "IgA" & SAMPLE == "-1h")

# Create model using only silent mutations and ignore multiple mutations
sub_model <- createSubstitutionMatrix(db, model="S")
mut_model <- createMutabilityMatrix(db, sub_model, model="S")
ext_model <- extendMutabilityMatrix(mut_model)
# }
# NOT RUN {
# }