In rforbiodatascience22/group_17_package:

title: "Group 17" output: rmarkdown::pdf_document vignette: > %\VignetteIndexEntry{vignette} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

library(group17)

Package Group 17

Introduction{#intro}

This package is builed around the central dogma of Molecular Biology, which describes the transfer of sequential information from DNA, RNA to Amino Acids (Crick, 1970). With the package you are able to generate and translate DNA, RNA and Amino-Acid Sequences. Further it enables you to perform basic statistic on those sequences.

Get started{#start}

The R-package group17 can be found on Github.

Installation{#inst}

To install group17 from GitHub repository run the code below:

library(devtools)
# install package from github
devtools::install_github("rforbiodatascience22/group_17_package")

Load the library

library(group17)

data = get(load("/cloud/project/data/rna_codons.rda"))
data

Methods{#methods}

Function 1{#fun1} : F1_form_DNA

To form a string of DNA base "A", "T", "G", "C" by random nucleotide selection following target length(size), default is 1.

form_dna <- function(size = 1){
  random_dna1 <- sample(c("A", "T", "G", "C"), size = size, replace = TRUE)
  random_dna2 <- paste0(random_dna1, collapse = "")
  return(random_dna2)
}

Function 2{#fun2} : F2_transcribe

To convert DNA base, "T" into "U" and getting mRNA as character.

transcribe <- function(DNA_seq){
  mRNA <- gsub("T", "U", DNA_seq)
  return(mRNA)
}

Function 3{#fun3} : F3_get_codon

To convert mRNA sequence composing of "A", "T", "G", "C" to condon like "AUGC"as character.

get_codons <- function(mRNA_seq, start = 1){
  mRNA_sequences <- nchar(mRNA_seq)
  codons <- substring(mRNA_seq,
                      first = seq(from = start, to = mRNA_seq_len-3+1, by = 3),
                      last = seq(from = 3+start-1, to = mRNA_seq_len, by = 3))
  return(codons)
}

Function 4{#fun4} : F4_translate

To use the data table "codonTable" to translate codons into amino acids and then return it as a sting.

translate <- function(codons){
  amino_acid <- paste0(codon_table[codons], collapse = "")
  return(amino_acid)
}

Plot occurence of Bases{#fun5} : F5_plot_base_occurence

To plot the occurence of Bases in a DNA, RNA or Amino Acid Sequence use plot_base_occurence()

seq <- "ACGTCCCCGGGT"
plot_base_occurrence(sequence = seq)

plot_base_occurrence <- function(sequence){
  unique_bases <- sequence %>%
    stringr::str_split(pattern = stringr::boundary("character"), simplify = TRUE) %>%
    as.character() %>%
    unique()

  counts <- sapply(unique_bases, function(count_occurence) stringr::str_count(string = sequence, pattern =  count_occurence)) %>%
    as.data.frame()

  colnames(counts) <- c("Counts")
  counts[["Base"]] <- rownames(counts)

  plot <- counts %>%
    ggplot2::ggplot(ggplot2::aes(x = Base, y = Counts, fill = Base)) +
    ggplot2::geom_col() +
    ggplot2::theme_bw()

  return(plot)
}