makeDegenerate5merMut - Make a degenerate 5-mer mutability model based on a 1-mer mutability model

## Description¶

`makeDegenerate5merMut` populates mutability rates from a 1-mer mutability model into 5-mers with corresponding central 1-mers.

## Usage¶

``````makeDegenerate5merMut(mut1mer, extended = FALSE)
``````

## Arguments¶

mut1mer
a named vector of length 4 containing (normalized) mutability rates. Names should correspond to nucleotides, which should include “A”, “T”, “G”, and “C” (case-insensitive).
extended
whether to return the unextended (`extended=FALSE`) or extended (`extended=TRUE`) 5-mer mutability model. Default is `FALSE`.

## Value¶

For `extended=FALSE`, a vector of length 1024. The vector returned is normalized. For `extended=TRUE`, a vector of length 3125.

## Details¶

As a concrete example, consider a 1-mer mutability model in which mutability rates of “A”, “T”, “G”, and “C” are, respectively, 0.14, 0.23, 0.31, and 0.32. In the resultant degenerate 5-mer mutability model, all the 5-mers that have an “A” as their central 1-mer would have mutability rate of 0.14/256, where 256 is the number of such 5-mers.

When `extended=TRUE`, `extendMutabilityMatrix` is called to extend the mutability vector of length 1024 into a vector of length 3125.

## Examples¶

``````# Make a degenerate 5-mer model (length of 1024) based on a 1-mer model
example1merMut <- c(A=0.2, T=0.1, C=0.4, G=0.3)
degenerate5merMut <- makeDegenerate5merMut(mut1mer = example1merMut)

# Look at a few 5-mers
degenerate5merMut[c("AAAAT", "AACAT", "AAGAT", "AATAT")]

``````
``````      AAAAT       AACAT       AAGAT       AATAT
0.000781250 0.001562500 0.001171875 0.000390625

``````
``````
# Normalized
sum(degenerate5merMut)
``````
``````[1] 1

``````

## See also¶

See makeAverage1merMut for making a 1-mer mutability model by taking the average of a 5-mer mutability model. See extendMutabilityMatrix for extending the mutability vector.