Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.
R-Forge SVN README
(See "http://download.r-forge.r-project.org/manuals/R-Forge_Manual.pdf"
for detailed information on registering a new project.)
1. Introduction
-----------------------------------------------------------------------
R is free software distributed under a GNU-style copyleft. R-Forge is
a central platform for the development of R packages, R-related
software and further projects. Among many other web-based features it
provides facilities for collaborative source code management via
Subversion (SVN).
2. The directory you're in
-----------------------------------------------------------------------
This is the repository of your project. It contains two important
pre-defined directories namely 'pkg' and 'www'. These directories must
not be deleted otherwise R-Forge's core functionality will not be
available (i.e., daily checking and building of your package or the
project websites).
'pkg' and 'www' are standardized and therefore are going to be
described in this README. The rest of your repository can be used as
you like.
3. 'pkg' directory
-----------------------------------------------------------------------
To make use of the package building and checking feature the package
source code has to be put into the 'pkg' directory of your repository
(i.e., 'pkg/DESCRIPTION', 'pkg/R', 'pkg/man', etc.) or, alternatively,
a subdirectory of 'pkg'. The latter structure allows for having more
than one package in a single project, e.g., if a project consists of
the packages foo and bar then the source code will be located in
'pkg/foo' and 'pkg/bar', respectively.
R-Forge automatically examines the 'pkg' directory of every repository
and builds the package sources as well as the package binaries on a
daily basis for Mac OSX and Windows (if applicable). The package builds
are provided in the 'R Packages' tab for download or can be installed
directly in R from a CRAN-style repository using
'install.packages("foo", repos="http://R-Forge.R-project.org")'.
Furthermore, in the 'R Packages' tab developers can examine logs
generated by the build and check process on different platforms.
4. 'www' directory
-----------------------------------------------------------------------
Developers may present their work on a subdomain of R-Forge, e.g.,
'http://foo.R-Forge.R-project.org', or via a link to an external
website.
This directory contains the project homepage which gets updated hourly
on R-Forge, so please take into consideration that it will not be
available right after you commit your changes or additions.
5. Help
-----------------------------------------------------------------------
If you need help don't hesitate to contact us at [email protected]