plaid.grid: Parameter Grid for BCPlaid Biclustering

Description Usage Arguments Value Author(s) See Also Examples

View source: R/ensemble.R

Description

Generates a list containing parameter settings for the ensemble algorithm.

Usage

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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

1

Example output

Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: lattice
[[1]]
[[1]]$method
[1] "BCPlaid"

[[1]]$cluster
[1] "b"

[[1]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[1]]$background
[1] TRUE

[[1]]$background.layer
[1] NA

[[1]]$background.df
[1] 1

[[1]]$row.release
[1] 0.5

[[1]]$col.release
[1] 0.5

[[1]]$shuffle
[1] 3

[[1]]$back.fit
[1] 0

[[1]]$max.layers
[1] 20

[[1]]$iter.startup
[1] 5

[[1]]$iter.layer
[1] 10

[[1]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[2]]
[[2]]$method
[1] "BCPlaid"

[[2]]$cluster
[1] "b"

[[2]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[2]]$background
[1] TRUE

[[2]]$background.layer
[1] NA

[[2]]$background.df
[1] 1

[[2]]$row.release
[1] 0.6

[[2]]$col.release
[1] 0.5

[[2]]$shuffle
[1] 3

[[2]]$back.fit
[1] 0

[[2]]$max.layers
[1] 20

[[2]]$iter.startup
[1] 5

[[2]]$iter.layer
[1] 10

[[2]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[3]]
[[3]]$method
[1] "BCPlaid"

[[3]]$cluster
[1] "b"

[[3]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[3]]$background
[1] TRUE

[[3]]$background.layer
[1] NA

[[3]]$background.df
[1] 1

[[3]]$row.release
[1] 0.7

[[3]]$col.release
[1] 0.5

[[3]]$shuffle
[1] 3

[[3]]$back.fit
[1] 0

[[3]]$max.layers
[1] 20

[[3]]$iter.startup
[1] 5

[[3]]$iter.layer
[1] 10

[[3]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[4]]
[[4]]$method
[1] "BCPlaid"

[[4]]$cluster
[1] "b"

[[4]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[4]]$background
[1] TRUE

[[4]]$background.layer
[1] NA

[[4]]$background.df
[1] 1

[[4]]$row.release
[1] 0.5

[[4]]$col.release
[1] 0.6

[[4]]$shuffle
[1] 3

[[4]]$back.fit
[1] 0

[[4]]$max.layers
[1] 20

[[4]]$iter.startup
[1] 5

[[4]]$iter.layer
[1] 10

[[4]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[5]]
[[5]]$method
[1] "BCPlaid"

[[5]]$cluster
[1] "b"

[[5]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[5]]$background
[1] TRUE

[[5]]$background.layer
[1] NA

[[5]]$background.df
[1] 1

[[5]]$row.release
[1] 0.6

[[5]]$col.release
[1] 0.6

[[5]]$shuffle
[1] 3

[[5]]$back.fit
[1] 0

[[5]]$max.layers
[1] 20

[[5]]$iter.startup
[1] 5

[[5]]$iter.layer
[1] 10

[[5]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[6]]
[[6]]$method
[1] "BCPlaid"

[[6]]$cluster
[1] "b"

[[6]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[6]]$background
[1] TRUE

[[6]]$background.layer
[1] NA

[[6]]$background.df
[1] 1

[[6]]$row.release
[1] 0.7

[[6]]$col.release
[1] 0.6

[[6]]$shuffle
[1] 3

[[6]]$back.fit
[1] 0

[[6]]$max.layers
[1] 20

[[6]]$iter.startup
[1] 5

[[6]]$iter.layer
[1] 10

[[6]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[7]]
[[7]]$method
[1] "BCPlaid"

[[7]]$cluster
[1] "b"

[[7]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[7]]$background
[1] TRUE

[[7]]$background.layer
[1] NA

[[7]]$background.df
[1] 1

[[7]]$row.release
[1] 0.5

[[7]]$col.release
[1] 0.7

[[7]]$shuffle
[1] 3

[[7]]$back.fit
[1] 0

[[7]]$max.layers
[1] 20

[[7]]$iter.startup
[1] 5

[[7]]$iter.layer
[1] 10

[[7]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[8]]
[[8]]$method
[1] "BCPlaid"

[[8]]$cluster
[1] "b"

[[8]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[8]]$background
[1] TRUE

[[8]]$background.layer
[1] NA

[[8]]$background.df
[1] 1

[[8]]$row.release
[1] 0.6

[[8]]$col.release
[1] 0.7

[[8]]$shuffle
[1] 3

[[8]]$back.fit
[1] 0

[[8]]$max.layers
[1] 20

[[8]]$iter.startup
[1] 5

[[8]]$iter.layer
[1] 10

[[8]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"



[[9]]
[[9]]$method
[1] "BCPlaid"

[[9]]$cluster
[1] "b"

[[9]]$fit.model
y ~ m + a + b
<environment: 0x52e0fd8>

[[9]]$background
[1] TRUE

[[9]]$background.layer
[1] NA

[[9]]$background.df
[1] 1

[[9]]$row.release
[1] 0.7

[[9]]$col.release
[1] 0.7

[[9]]$shuffle
[1] 3

[[9]]$back.fit
[1] 0

[[9]]$max.layers
[1] 20

[[9]]$iter.startup
[1] 5

[[9]]$iter.layer
[1] 10

[[9]]$verbose
[1] FALSE

attr(,"out.attrs")
attr(,"out.attrs")$dim
          method          cluster        fit.model       background 
               1                1                1                1 
background.layer    background.df      row.release      col.release 
               1                1                3                3 
         shuffle         back.fit       max.layers     iter.startup 
               1                1                1                1 
      iter.layer          verbose 
               1                1 

attr(,"out.attrs")$dimnames
attr(,"out.attrs")$dimnames$method
[1] "method=BCPlaid"

attr(,"out.attrs")$dimnames$cluster
[1] "cluster=b"

attr(,"out.attrs")$dimnames$fit.model
[1] "fit.model=y ~ m + a + b"

attr(,"out.attrs")$dimnames$background
[1] "background=TRUE"

attr(,"out.attrs")$dimnames$background.layer
[1] "background.layer=NA"

attr(,"out.attrs")$dimnames$background.df
[1] "background.df=1"

attr(,"out.attrs")$dimnames$row.release
[1] "row.release=0.5" "row.release=0.6" "row.release=0.7"

attr(,"out.attrs")$dimnames$col.release
[1] "col.release=0.5" "col.release=0.6" "col.release=0.7"

attr(,"out.attrs")$dimnames$shuffle
[1] "shuffle=3"

attr(,"out.attrs")$dimnames$back.fit
[1] "back.fit=0"

attr(,"out.attrs")$dimnames$max.layers
[1] "max.layers=20"

attr(,"out.attrs")$dimnames$iter.startup
[1] "iter.startup=5"

attr(,"out.attrs")$dimnames$iter.layer
[1] "iter.layer=10"

attr(,"out.attrs")$dimnames$verbose
[1] "verbose=FALSE"

biclust documentation built on May 25, 2021, 5:09 p.m.

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