createMutationDefinition - 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 charactersc("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.
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)
See also¶
See MutationDefinition for the return object.