How To Install r-cran-qtl on Ubuntu 18.04
Introduction
In this tutorial we learn how to install r-cran-qtl on Ubuntu 18.04.
What is r-cran-qtl
r-cran-qtl is:
R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental crosses. It is implemented as an add-on-package for the freely available and widely used statistical language/software R (see http://www.r-project.org).
The development of this software as an add-on to R allows one to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R. Further, the user will benefit by the seamless integration of the QTL mapping software into a general statistical analysis program. The goal is to make complex QTL mapping methods widely accessible and allow users to focus on modeling rather than computing.
A key component of computational methods for QTL mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data. The main HMM algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses were implemented.
The current version of R/qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with the EM algorithm), Haley-Knott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). One may also fit higher-order QTL models by multiple imputation.
There are three methods to install r-cran-qtl on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install r-cran-qtl Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install r-cran-qtl using apt-get by running the following command:
sudo apt-get -y install r-cran-qtl
Install r-cran-qtl Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-cran-qtl using apt by running the following command:
sudo apt -y install r-cran-qtl
Install r-cran-qtl Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install r-cran-qtl using aptitude by running the following command:
sudo aptitude -y install r-cran-qtl
How To Uninstall r-cran-qtl on Ubuntu 18.04
To uninstall only the r-cran-qtl package we can use the following command:
sudo apt-get remove r-cran-qtl
Uninstall r-cran-qtl And Its Dependencies
To uninstall r-cran-qtl and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove r-cran-qtl
Remove r-cran-qtl Configurations and Data
To remove r-cran-qtl configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge r-cran-qtl
Remove r-cran-qtl configuration, data, and all of its dependencies
We can use the following command to remove r-cran-qtl configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-cran-qtl
References
Summary
In this tutorial we learn how to install r-cran-qtl package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
