calculateMutability - Calculate total mutability

Description

calculateMutability calculates the total (summed) mutability for a set of sequences based on a 5-mer nucleotide mutability model.

Usage

calculateMutability(sequences, model = HH_S5F, progress = FALSE)

Arguments

sequences
character vector of sequences.
model
TargetingModel object with mutation likelihood information.
progress
if TRUE print a progress bar.

Value

Numeric vector with a total mutability score for each sequence.

Examples

# Subset example data to one isotype and sample as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, ISOTYPE == "IgA" & SAMPLE == "-1h")

# Calculate mutability of germline sequences using \link{HH_S5F} model
mutability <- calculateMutability(sequences=db$GERMLINE_IMGT_D_MASK, model=HH_S5F)