/bioseq

R package to work on basic sequence data.

Primary LanguageROtherNOASSERTION

Bioseq: A basic package on sequences

Note: This is very simple and basic package, purely as my kick-starter code for working on creating a package.

Installation

  • Option 1 via devtools
$ R
  • In R interface of your choice
> install.packages("devtools")
> library(devtools)

> install.github("idlip/bioseq")
> library(bioseq)
  • Option 2 via tar.gz or zip file from this Git repo.
install.packages("<path/to/bioseq>.tar.gz", repos=NULL)

Usage

  • For any function, you can list them bioseq::<tab> by hitting tab.
  • You can refer for documentation/man page via ?bioseq, ?bioseq_complement…

bioseq()

  • An interactive function with no arguments required.
  • It prompts for user to input DNA sequence data, and provides option to give All (A) details, Complementary (C), Transcript (T) or Reverse (R) complement.

bioseq_complement(seq)

  • Takes 1 argument as DNA sequence and give the return value as characters of complementary strand.

bioseq_rcomplement(seq)

  • Takes 1 argument as DNA sequence and provide the reverse complement of it.

bioseq_transcribe(seq)

  • Takes 1 argument as DNA sequence and return the mRna transcript of the sequence.

Plans [0/2]

  • [ ] Make the package DNA agnostic, so it works on RNA and also protein sequence.
  • [ ] Add more basic functions to get minimal things done.