## R/qtl2 QTL analysis for high-dimensional data and complex crosses

R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software
R/qtl, to better handle high-dimensional data
and complex cross designs. It is split
into qtl2geno (for calculating
genotype probabilities, imputations, and genetic maps),
qtl2scan (for QTL genome scans and
related calculations), and
qtl2plot (for data visualization).
A further package, qtl2convert,
contains functions for converting data among the R/qtl2,
DOQTL,
and R/qtl formats, for example to convert genotype
probabilities produced by DOQTL to the format needed by qtl2scan, or
to convert qtl2scan results to the format produced by `scanone`

in
R/qtl, so that they may be graphed with the R/qtl functions.

In R/qtl2 version 0.5, we made major revisions to some of the
central data structures, and a number of steps in QTL analyses have
changed. See the revised
user guide, or
this description of the changes in version 0.5.
A couple of functions for converting objects from the format for
Rqtl2 version 0.4 and the new format are in
`convert_04_to_05.R`

.

### Installation

R/qtl2 is early in development and so is not yet available on CRAN.

You can install R/qtl2 from GitHub.

You first need to install the devtools package, plus a set of package dependencies: yaml, jsonlite, data.table, and RcppEigen. (Additional, secondary dependencies will also be installed)

```
install.packages(c("devtools", "yaml", "jsonlite", "data.table", "RcppEigen"))
```

Then, install R/qtl2 using `devtools::install_github()`

.

```
library(devtools)
install_github(paste0("rqtl/qtl2", c("geno", "scan", "plot", "convert")))
```

### Vignettes

- user guide
- input file formats (also see the sample data files and the qtl2data repository)
- differences between R/qtl and R/qtl2
- developer guide
- HMM benchmarks
- linear regression benchmarks

### License

The qtl2geno, qtl2scan, qtl2plot, and qtl2convert packages are free software; you can redistribute them and/or modify them under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

These programs are distributed in the hope that they will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

Sources on github: