extendMutabilityMatrix: Extends a mutability model to include Ns.

In shazam: Immunoglobulin Somatic Hypermutation Analysis

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 MutabilityModel containing 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).

If the input mutabilityModel is of class MutabilityModel, then the output MutabilityModel will carry over the input numMutS and numMutR slots.

See Also

createMutabilityMatrix, extendSubstitutionMatrix, MutabilityModel

Examples

# Subset example data to one isotype and sample as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, c_call == "IGHA" & sample_id == "-1h")
set.seed(112)
db <- dplyr::slice_sample(db, n=75)

# Create model using only silent mutations and ignore multiple 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")
ext_model <- extendMutabilityMatrix(mut_model)

shazam documentation built on Oct. 3, 2023, 1:06 a.m.