Lars Snipen and Kristian Liland
Install the package from CRAN (https://cran.r-project.org/) in the standard way, either by
install.packages("microseq")or by using the Tools - Install Packages… menu in RStudio.
Or, install from GitHub by
devtools::install_github("larssnip/microseq")Obviously, you need the devtools package from CRAN first.
There are plenty of R packages with functions for handling sequence
data. However, many of them insists on storing sequences in special data
types, usually variants of a list. This is an idea inherited from
object oriented programming, but R is made to work with tables, and
the object oriented approach is more useful in other languages,
e.g. Python.
An idea behind this package is to keep sequence data in the generic data structures in R instead of creating new and complex data types. This makes it possible to use the power of standard data wrangling tools that R-users are familiar with.
Both FASTA and FASTQ files are read into tables, and sequences are
stored as texts. This makes it straightforward to use all the tools
available in packages like dplyr and stringr, for data wrangling and
string manipulations. Both input and output FASTA or FASTQ files may be
gzipped, no need for uncompressions.
Functions for findings ORFs or genes findOrfs(), findrRNA(),
findGenes() return results as GFF-formatted tables, i.e. a standard
tibble with either texts or numbers in the columns.
Many bioinformatic softwares produces results as tables, if you let them. Reading, wrangling and plotting data in tables is what R does best!
This toolbox is very much geared towards what we have found useful in microbial genomics.
Some functions in this package calls upons external software that must be available on the system. Some of these are ‘installed’ by simply downloading a binary executable that you put somewhere proper on your computer. To make such programs visible to R, you typically need to update your PATH environment variable, to specify where these executables are located. Try it out, and use google for help!
The functions msalign() and muscle() uses the free software
muscle
(https://www.drive5.com/muscle/). From the website you download (and
unzip) an executable. NB! Change its name to
muscle, no more and no less (i.e. no
version numbers etc). In the R console the command
system("muscle -h")should produce some sensible output.
The function findrRNA() uses the free software
barrnap
(https://github.com/tseemann/barrnap). The GitHub site explains how to
install. In the R console the command
system("barrnap -h")should produce some sensible output.
The function findGenes() uses the free software
prodigal
(https://github.com/hyattpd/Prodigal). The GitHub site explains how to
install. In the R console the command
system("prodigal -h")should produce some sensible output.