In rforbiodatascience22/group_5_package: DOgma - The Central Dogma is cool

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DOgma

Group 5: Astrid (s184248), Caroline (s183493), Christian (s165476), Frederik (s184260) and Nils (s220672)

devtools::load_all()
library(DOgma)

Dogma is an R package meant to mimic the molecular dogma of biology. Thus, DOgma can be used to translate DNA to RNA and then translate the RNA sequence to a protein sequence by using the 64 different codons of the genetic code. The package contains 5 different functions: "DNA_generator","DNA_to_RNA", "sequence_to_codons","export_codons" and "AA_abundance". The first function "DNA_generator" can be used to generate a random DNA sequence of a specified length.

DNA_seq <- DNA_generator(12)
DNA_seq

The next function "DNA_to_RNA" translates the DNA sequence into an RNA sequence.

RNA_seq <- DNA_to_RNA(DNA_seq)
RNA_seq

The RNA codons can then be generated from the RNA sequence by using the function sequence_to_codons.

codons <- sequence_to_codons(RNA_seq)
codons

These generated codons can then be used to translate the RNA sequence into a protein sequence by using the function "export_amino_acid".

prot_seq <- export_amino_acid(codons)
prot_seq

The abundance of each amino acid in the genreated protien sequence can then be analysed and graphed using the function AA_abundance.

aa_abundance_graph <- AA_abundance(prot_seq)
aa_abundance_graph

The package has multiple use cases, one of which is analysing the abundances of amino acids in protein sequences. However, the package can also be used only to translate DNA sequences to protein sequences. The library limits the use of dependencies to make sure that the user does not have way to many functions added to their NAMESPACE to limit confusion. Furthermore, instead of using the "\@importFrom package function" the function from other libraries will be using the package::function() syntax. This verifies both that the function is called directly fromthe correct package and that it does not call function() from the NAMESPACE of the user.

rforbiodatascience22/group_5_package documentation built on April 7, 2022, 8:20 p.m.