R: Tuning functions for multilevel sPLS method

tune.splslevel {mixOmics} | R Documentation

## Tuning functions for multilevel sPLS method

### Description

For a multilevel spls analysis, the tuning criterion is based on the maximisation of the correlation between the components from both data sets

### Usage

    tune.splslevel(X, Y, multilevel, ncomp = NULL,
    mode = "regression",
    test.keepX = rep(ncol(X), ncomp),
    test.keepY = rep(ncol(Y), ncomp),
    already.tested.X = NULL,
    already.tested.Y = NULL)

### Arguments

`X` | numeric matrix of predictors. `NA`s are allowed.
`Y` | `if(method = 'spls')` numeric vector or matrix of continuous responses (for multi-response models) `NA`s are allowed.
`multilevel` | Design matrix for multilevel analysis (for repeated measurements) that indicates the repeated measures on each individual, i.e. the individuals ID. See Details.
`ncomp` | the number of components to include in the model.
`mode` | character string. What type of algorithm to use, (partially) matching one of `"regression"`, `"canonical"`, `"invariant"` or `"classic"`.
`test.keepX` | numeric vector for the different number of variables to test from the X data set
`test.keepY` | numeric vector for the different number of variables to test from the Y data set
`already.tested.X` | Optional, if `ncomp > 1` A numeric vector indicating the number of variables to select from the X data set on the firsts components.
`already.tested.Y` | Optional, if `ncomp > 1` A numeric vector indicating the number of variables to select from the Y data set on the firsts components.

### Details

For a multilevel spls analysis, the tuning criterion is based on the maximisation of the correlation between the components from both data sets

### Value

`cor.value` | correlation between latent variables

### Author(s)

Kim-Anh Lê Cao, Benoit Gautier, Francois Bartolo, Florian Rohart.

### References

mixOmics article:

Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752

### See Also

`splsda`, `predict.splsda` and http://www.mixOmics.org for more details.

### Examples

    data(liver.toxicity)
    # note: we made up those data, pretending they are repeated measurements
    repeat.indiv <- c(1, 2, 1, 2, 1, 2, 1, 2, 3, 3, 4, 3, 4, 3, 4, 4, 5, 6, 5, 5,
    6, 5, 6, 7, 7, 8, 6, 7, 8, 7, 8, 8, 9, 10, 9, 10, 11, 9, 9,
    10, 11, 12, 12, 10, 11, 12, 11, 12, 13, 14, 13, 14, 13, 14,
    13, 14, 15, 16, 15, 16, 15, 16, 15, 16)
    summary(as.factor(repeat.indiv)) # 16 rats, 4 measurements each

    # this is a spls (unsupervised analysis) so no need to mention any factor in design
    # we only perform a one level variation split
    design <- data.frame(sample = repeat.indiv)

    tune.splslevel(X = liver.toxicity$gene,
    Y=liver.toxicity$clinic,
    multilevel = design,
    test.keepX = c(5,10,15),
    test.keepY = c(1,2,5),
    ncomp = 1)

[Package mixOmics version 6.3.2 Index]