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.
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")
# Create model using only silent mutations
sub_model <- createSubstitutionMatrix(db, sequenceColumn="sequence_alignment",
germlineColumn="germline_alignment_d_mask",
vCallColumn="v_call",model="s")
ext_model <- extendSubstitutionMatrix(sub_model)