shazam (version 1.2.0)

createMutationDefinition: Creates a MutationDefinition

Description

createMutationDefinition creates a MutationDefinition.

Usage

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

Value

A MutationDefinition object.

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.

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)