calculateMutability: Calculate total mutability

In shazam: Immunoglobulin Somatic Hypermutation Analysis

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, c_call == "IGHA" & sample_id == "-1h")

# Calculate mutability of germline sequences using \link{HH_S5F} model
mutability <- calculateMutability(sequences=db[["germline_alignment_d_mask"]], model=HH_S5F)

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