makeAverage1merMut: Make a 1-mer mutability model by averaging over a 5-mer...

In shazam: Immunoglobulin Somatic Hypermutation Analysis

Make a 1-mer mutability model by averaging over a 5-mer mutability model

Description

makeAverage1merMut averages mutability rates in a 5-mer mutability model to derive a 1-mer mutability model.

Usage

makeAverage1merMut(mut5mer)

Arguments

mut5mer

a named vector of length 1024 such as that returned by createMutabilityMatrix and that returned by makeDegenerate5merMut with extended=FALSE. Names should correspond to 5-mers made up of "A", "T", "G", and "C" (case-insensitive). NA values are allowed.

Details

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.

Value

A named vector of length 4 containing normalized mutability rates.

See Also

See makeDegenerate5merMut for making a degenerate 5-mer mutability model based on a 1-mer mutability model.

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)
 
# Now make a 1-mer model by averaging over the degenerate 5-mer model
# Expected to get back example1merMut
makeAverage1merMut(mut5mer = degenerate5merMut)

shazam documentation built on Oct. 3, 2023, 1:06 a.m.