extendMutabilityMatrix - Extends a mutability model to include Ns.
extendMutabilityMatrix extends a 5-mer nucleotide mutability model
with 5-mers that include Ns by averaging over all corresponding 5-mers without Ns.
- vector of 5-mer mutability rates built by createMutabilityMatrix.
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
then the output
MutabilityModel will carry over the input
# Subset example data to one isotype and sample as a demo data(ExampleDb, package="alakazam") db <- subset(ExampleDb, c_call == "IGHA" & sample_id == "-1h") # 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")
Warning:Insufficient number of mutations to infer some 5-mers. Filled with 0.
ext_model <- extendMutabilityMatrix(mut_model)