makeAverage1merMut - Make a 1-mer mutability model by averaging over a 5-mer mutability model
makeAverage1merMut averages mutability rates in a 5-mer mutability model
to derive a 1-mer mutability model.
- a named vector of length 1024 such as that returned by
createMutabilityMatrixand that returned by
extended=FALSE. Names should correspond to 5-mers made up of “A”, “T”, “G”, and “C” (case-insensitive).
NAvalues are allowed.
A named vector of length 4 containing normalized mutability rates.
For example, the mutability rate of “A” in the resultant 1-mer model is derived by averaging the mutability rates of all the 5-mers that have an “A” as their central 1-mer, followed by normalization.
# 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) # Now make a 1-mer model by averaging over the degenerate 5-mer model # Expected to get back example1merMut makeAverage1merMut(mut5mer = degenerate5merMut)
A C G T 0.2 0.4 0.3 0.1
See makeDegenerate5merMut for making a degenerate 5-mer mutability model based on a 1-mer mutability model.