shazam (version 1.2.0)

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)

Value

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

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.

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.

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.

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")]

# Normalized
sum(degenerate5merMut)