#' @title Randomly delete nucleotides in a sequence
#'
#' @description Pass in a vector of nucleotides, the probability of single
#' nucleotide deletions for each of the four nucleotides, and return a new
#' vector of nucleotides.
#'
#' @param nt_sequence A vector of nucleotides, i.e. c("C","A","T","G","A").
#' @param deletion_rate_A The probability of an "A" deletion occurring.
#' @param deletion_rate_T The probability of an "T" deletion occurring.
#' @param deletion_rate_C The probability of an "C" deletion occurring.
#' @param deletion_rate_G The probability of an "G" deletion occurring.
#'
#' @importFrom assertthat assert_that is.number noNA
#'
#' @return A vector of nucleotides, i.e. c("C","T","G","A"), with deleted
#' nucleotides omitted.
#'
#' @examples
#' set.seed(1)
#' deletion_mutator(
#' c("C","A","T","G","A"),
#' deletion_rate_A = 0.05,
#' deletion_rate_T = 0.05,
#' deletion_rate_C = 0.05,
#' deletion_rate_G = 0.05
#' )
#'
#' @export
deletion_mutator <- function(
nt_sequence,
deletion_rate_A = 0.05,
deletion_rate_T = 0.05,
deletion_rate_C = 0.05,
deletion_rate_G = 0.05
){
# Perform type checking.
assert_that(
is.vector(nt_sequence) &&
(class(nt_sequence) == "character") &&
noNA(nt_sequence) &&
all(nt_sequence %in% c("A","T","C","G")) &&
length(nt_sequence) > 0
)
assert_that(
is.number(deletion_rate_A) &&
(class(deletion_rate_A) == "numeric") &&
noNA(deletion_rate_A) &&
(deletion_rate_A >= 0) && (deletion_rate_A <= 1)
)
assert_that(
is.number(deletion_rate_T) &&
(class(deletion_rate_T) == "numeric") &&
noNA(deletion_rate_T) &&
(deletion_rate_T >= 0) && (deletion_rate_T <= 1)
)
assert_that(
is.number(deletion_rate_C) &&
(class(deletion_rate_C) == "numeric") &&
noNA(deletion_rate_C) &&
(deletion_rate_C >= 0) && (deletion_rate_C <= 1)
)
assert_that(
is.number(deletion_rate_G) &&
(class(deletion_rate_G) == "numeric") &&
noNA(deletion_rate_G) &&
(deletion_rate_G >= 0) && (deletion_rate_G <= 1)
)
# Call .deletion_mutator_cpp
.deletion_mutator_cpp(
nt_sequence,
deletion_rate_A,
deletion_rate_T,
deletion_rate_C,
deletion_rate_G
)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.