plaid.grid: Parameter Grid for BCPlaid Biclustering

In biclust: BiCluster Algorithms

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 stimates 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 [e-mail]

See Also

ensemble, BCPlaid

Examples

plaid.grid()

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 2, 2019, 5:56 p.m.