R: Parameter Grid for BCPlaid Biclustering

plaid.grid {biclust} | R Documentation

## Parameter Grid for BCPlaid Biclustering

### Description

Generates a list containing parameter settings for the ensemble algorithm.

### Usage

    plaid.grid(method = "BCPlaid", cluster = "b", fit.model = y ~ m + a + b,
      background = TRUE, background.layer = NA, background.df = 1,
      row.release = c(0.5, 0.6, 0.7), col.release = c(0.5, 0.6, 0.7),
      shuffle = 3, back.fit = 0, max.layers = 20, iter.startup = 5,
      iter.layer = 10, verbose = FALSE)

### Arguments

`method` | Here BCPlaid, to perform Plaid algorithm
`cluster` | 'r', 'c' or 'b', to cluster rows, columns or both (default 'b')
`fit.model` | Model (formula) to fit each layer. Usually, a linear model is used, that estimates three parameters: m (constant for all elements in the bicluster), a(contant for all rows in the bicluster) and b (constant for all columns). Thus, default is: y ~ m + a + b.
`background` | If 'TRUE' the method will consider that a background layer (constant for all rows and columns) is present in the data matrix.
`background.layer` | If background='TRUE' a own background layer (Matrix with dimension of x) can be specified.
`background.df` | Degrees of Freedom of backround layer if background.layer is specified.
`shuffle` | Before a layer is added, it's statistical significance is compared against a number of layers obtained by random defined by this parameter. Default is 3, higher numbers could affect time performance.
`iter.startup` | Number of iterations to find starting values
`iter.layer` | Number of iterations to find each layer
`back.fit` | After a layer is added, additional iterations can be done to refine the fitting of the layer (default set to 0)
`row.release` | Scalar in [0,1](with interval recommended [0.5-0.7]) used as threshold to prune rows in the layers depending on row homogeneity
`col.release` | As above, with columns
`max.layers` | Maximum number of layer to include in the model
`verbose` | If 'TRUE' prints extra information on progress.

### Value

A list containing parameter settings

### Author(s)

Sebastian Kaiser sebastian.kaiser@stat.uni-muenchen.de

### See Also

`ensemble`, `BCPlaid`

### Examples

    plaid.grid()

[Package biclust version 2.0.2 Index]