Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/wrapper.rgcca.R

Wrapper function to perform Regularized Generalised Canonical Correlation Analysis (rGCCA), a generalised approach for the integration of multiple datasets. For more details, see the `help(rgcca)`

from the RGCCA package.

1 2 3 4 5 6 7 8 9 10 11 12 13 |

`X` |
a list of data sets (called 'blocks') matching on the same samples. Data in the list should be arranged in samples x variables. |

`design` |
numeric matrix of size (number of blocks in X) x (number of blocks in X) with values between 0 and 1. Each value indicates the strenght of the relationship to be modelled between two blocks using sGCCA; a value of 0 indicates no relationship, 1 is the maximum value. If |

`tau` |
numeric vector of length the number of blocks in |

`ncomp` |
the number of components to include in the model. Default to 1. |

`keepX` |
A vector of same length as X. Each entry keepX[i] is the number of X[[i]]-variables kept in the model. |

`scheme` |
Either "horst", "factorial" or "centroid" (Default: "horst"). |

`scale` |
boleean. If scale = TRUE, each block is standardized to zero means and unit variances (default: TRUE) |

`init` |
Mode of initialization use in the algorithm, either by Singular Value Decompostion of the product of each block of X with Y ("svd") or each block independently ("svd.single") . Default to "svd.single". |

`tol` |
Convergence stopping value. |

`max.iter` |
integer, the maximum number of iterations. |

`near.zero.var` |
boolean, see the internal |

`all.outputs` |
boolean. Computation can be faster when some specific (and non-essential) outputs are not calculated. Default = |

This wrapper function performs rGCCA (see RGCCA) with *1, … ,*`ncomp`

components on each block data set.
A supervised or unsupervised model can be run. For a supervised model, the `unmap`

function should be used as an input data set.
More details can be found on the package RGCCA.

`wrapper.rgcca`

returns an object of class `"rgcca"`

, a list
that contains the following components:

`data` |
the input data set (as a list). |

`design` |
the input design. |

`variates` |
the sgcca components. |

`loadings` |
the loadings for each block data set (outer wieght vector). |

`loadings.star` |
the laodings, standardised. |

`tau` |
the input tau parameter. |

`scheme` |
the input schme. |

`ncomp` |
the number of components included in the model for each block. |

`crit` |
the convergence criterion. |

`AVE` |
Indicators of model quality based on the Average Variance Explained (AVE): AVE(for one block), AVE(outer model), AVE(inner model).. |

`names` |
list containing the names to be used for individuals and variables. |

More details can be found in the references.

Arthur Tenenhaus, Vincent Guillemot and Kim-Anh Lê Cao.

Tenenhaus A. and Tenenhaus M., (2011), Regularized Generalized Canonical Correlation Analysis, Psychometrika, Vol. 76, Nr 2, pp 257-284.

Schafer J. and Strimmer K., (2005), A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statist. Appl. Genet. Mol. Biol. 4:32.

`wrapper.rgcca`

, `plotIndiv`

, `plotVar`

, `wrapper.sgcca`

and http://www.mixOmics.org for more details.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
data(nutrimouse)
# need to unmap the Y factor diet
Y = unmap(nutrimouse$diet)
data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid, Y = Y)
# with this design, gene expression and lipids are connected to the diet factor
# design = matrix(c(0,0,1,
# 0,0,1,
# 1,1,0), ncol = 3, nrow = 3, byrow = TRUE)
# with this design, gene expression and lipids are connected to the diet factor
# and gene expression and lipids are also connected
design = matrix(c(0,1,1,
1,0,1,
1,1,0), ncol = 3, nrow = 3, byrow = TRUE)
#note: the tau parameter is the regularization parameter
wrap.result.rgcca = wrapper.rgcca(X = data, design = design, tau = c(1, 1, 0),
ncomp = 2,
scheme = "centroid")
#wrap.result.rgcca
``` |

```
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2
Loaded mixOmics 6.3.2
Thank you for using mixOmics!
How to apply our methods: http://www.mixOmics.org for some examples.
Questions or comments: email us at mixomics[at]math.univ-toulouse.fr
Any bugs? https://bitbucket.org/klecao/package-mixomics/issues
Cite us: citation('mixOmics')
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
```

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