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


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


makeDegenerate5merMut(mut1mer, extended = FALSE)


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


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


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.


# 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
[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.