How To Install genotypes2m.txt.gz on Ubuntu 22.04

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install r-cran-qtl

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is genotypes2m.txt.gz and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 22.04. This guide was written specifically with a server running Ubuntu 22.04 in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install genotypes2m.txt.gz on Ubuntu 22.04. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install genotypes2m.txt.gz using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install genotypes2m.txt.gz using apt by running the following command:

sudo apt -y install r-cran-qtl

Install genotypes2m.txt.gz using apt

Because genotypes2m.txt.gz is available in Ubuntu 22.04’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install genotypes2m.txt.gz using apt by running the following command:

sudo apt -y install r-cran-qtl

Install genotypes2m.txt.gz 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 22.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install genotypes2m.txt.gz by running the following command:

sudo aptitude -y install r-cran-qtl

How to upgrade (update) a single package genotypes2m.txt.gz using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the genotypes2m.txt.gz, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install r-cran-qtl

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install r-cran-qtl

How To Uninstall genotypes2m.txt.gz from Ubuntu 22.04

To uninstall only the genotypes2m.txt.gz package you can execute the following command:

sudo apt-get remove r-cran-qtl

Uninstall genotypes2m.txt.gz and all its dependencies

To uninstall genotypes2m.txt.gz and its dependencies that are no longer needed by Ubuntu 22.04, you can use the command below:

sudo apt-get -y autoremove r-cran-qtl

Remove genotypes2m.txt.gz with all configurations and data

To remove genotypes2m.txt.gz configuration and data from your system you can run the following purge command:

sudo apt-get -y purge r-cran-qtl

Remove genotypes2m.txt.gz completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to genotypes2m.txt.gz package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge r-cran-qtl

Extra info and code examples

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.

Conclusion

You now have a full guide on how to install genotypes2m.txt.gz using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the genotypes2m.txt.gz from Ubuntu 22.04.

See also: