makeAverage1merSub

makeAverage1merSub - Make a 1-mer substitution model by averaging over a 5-mer substitution model

Description¶

makeAverage1merSub averages substitution rates in a 5-mer substitution model to derive a 1-mer substitution model.

Usage¶

makeAverage1merSub(sub5mer)

Arguments¶

sub5mer: a 4x1024 matrix such as that returned by createSubstitutionMatrix and that returned by makeDegenerate5merSub with extended=FALSE. Column names should correspond to 5-mers containing the central 1-mer to mutate from. Row names should correspond to nucleotides to mutate into. Nucleotides should include “A”, “T”, “G”, and “C” (case-insensitive).

Value¶

A 4x4 matrix with row names representing nucleotides to mutate from and column names representing nucleotides to mutate into. Rates are normalized by row.

Details¶

For example, the substitution rate from “A” to “T” in the resultant 1-mer model is derived by averaging the substitution rates into a “T” of all the 5-mers that have an “A” as their central 1-mer.

Examples¶

# Make a degenerate 5-mer model (4x1024) based on HKL_S1F (4x4)
degenerate5merSub <- makeDegenerate5merSub(sub1mer = HKL_S1F)

# Now make a 1-mer model by averaging over the degenerate 5-mer model
# Expected to get back HKL_S1F
makeAverage1merSub(sub5mer = degenerate5merSub)

     A    C    G    T
A   NA 0.26 0.50 0.24
C 0.25   NA 0.30 0.45
G 0.53 0.31   NA 0.16
T 0.20 0.57 0.23   NA