createMutationDefinition: Creates a MutationDefinition

In shazam: Immunoglobulin Somatic Hypermutation Analysis

Creates a MutationDefinition

Description

createMutationDefinition creates a MutationDefinition.

Usage

createMutationDefinition(name, classes, description = "", citation = "")

Arguments

name	name of the mutation definition.
classes	named character vectors with single-letter amino acid codes as names and amino acid classes as values, with NA assigned to set of characters c("X", "*", "-", "."). Replacement (R) is be defined as a change in amino acid class and silent (S) as no change in class.
description	description of the mutation definition and its source data.
citation	publication source.

Value

A MutationDefinition object.

See Also

See MutationDefinition for the return object.

Examples

# Define hydropathy classes
suppressPackageStartupMessages(library(alakazam))
hydropathy <- list(hydrophobic=c("A", "I", "L", "M", "F", "W", "V"),
                   hydrophilic=c("R", "N", "D", "C", "Q", "E", "K"),
                   neutral=c("G", "H", "P", "S", "T", "Y"))
chars <- unlist(hydropathy, use.names=FALSE)
classes <- setNames(translateStrings(chars, hydropathy), chars)

# Create hydropathy mutation definition
md <- createMutationDefinition("Hydropathy", classes)

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