README.md

In rforbiodatascience22/group_9_package: What the Package Does (One Line, Title Case)

library(CentralDogma)

Package Description

This package stimulates the process of the central dogma in biology, namely the process of replication, transcription and translation. Five main functions are included in this package so far.

Functions

• generate_DNA(): It takes a number as an input and randomly generate a corresponding number of DAN sequence.
• transcription(): It takes a DNA sequence as an input and returns the transcripted mRNA sequence as an output, which means all the “A”s are will be changed into “U”s.
• generate_codons(): It takes mRNA sequence as an input and generate the codon list.
• translation(): It takes a list of codons and translate each into corresponding amino acids.
• AA_num_plot(): It takes an amino acid sequence as an input and returns the bar plot reflecting the number of each unique AA in the input sequence. The plot is saved as a variable called “AAplot” in inside of the function.

Use Case

1. For transcription():

transcription("ATCTA")
#> [1] "AUCUA"

1. For AA_num_plot():

AAplot <- AA_num_plot("MFVVYNKRSS")
AAplot

Discussion for T4

• The dependencies are needed for the fifth function AA_num_plot(). We typed usethis::use_package(“package_name”) three times to add “ggplot”, “magrittr” and “stringr” into the DESCRIPTION file. Inside of the funcion file, we added @importFrom magrittr %>% in order to use the Tidyver pipe to our package namespace.

• Disadvantages for not limiting the number of dependencies:

  • Anyone installing your package must also install the dependency (which you’ve written about).
  • Anyone loading your package must also load all dependencies, even if only into “background” namespaces.
  • Your package’s code is affected by dependencies.

• package::function() Vs. @importFrom package function:

  • If you are using just a few functions from another package, then it’s better to note the package name in the Imports: field of the DESCRIPTION file and call the function(s) explicitly using ::, e.g., pkg::fun().
  • If you are using functions repeatedly, you can avoid :: by importing the function with @importFrom pkg fun.

rforbiodatascience22/group_9_package documentation built on March 25, 2022, 12:24 a.m.