makeDegenerate5merSub {shazam}

Make a degenerate 5-mer substitution model based on a 1-mer substitution model

Description

makeDegenerate5merSub populates substitution rates from a 1-mer substitution model into 5-mers with corresponding central 1-mers.

Usage

makeDegenerate5merSub(sub1mer, extended = FALSE)

Arguments

sub1mer

a 4x4 matrix containing (normalized) substitution rates. Row names should correspond to nucleotides to mutate from. Column names should correspond to nucleotides to mutate into. Nucleotides should include "A", "T", "G", and "C" (case-insensitive).

extended

whether to return the unextended (extended=FALSE) or extended (extended=TRUE) 5-mer substitution model. Default is FALSE.

Details

As a concrete example, consider a 1-mer substitution model in which substitution rates from "A" to "T", "G", and "C" are, respectively, 0.1, 0.6, and 0.3. In the resultant degenerate 5-mer substitution model, all the 5-mers (columns) that have an "A" as their central 1-mer would have substitution rates (rows) of 0.1, 0.6, and 0.3 to "T", "G", and "C" respectively.

When extended=TRUE, extendSubstitutionMatrix is called to extend the 4x1024 substitution matrix.

Value

For extended=FALSE, a 4x1024 matrix. For extended=TRUE, a 5x3125 matrix.

See Also

See makeAverage1merSub for making a 1-mer substitution model by taking the average of a 5-mer substitution model. See extendSubstitutionMatrix for extending the substitution matrix.

Examples

# Make a degenerate 5-mer model (4x1024) based on HKL_S1F (4x4)
# Note: not to be confused with HKL_S5F@substitution, which is non-degenerate
degenerate5merSub <- makeDegenerate5merSub(sub1mer = HKL_S1F)

# Look at a few 5-mers
degenerate5merSub[, c("AAAAT", "AACAT", "AAGAT", "AATAT")]