bibit_columnextension {BiBitR}R Documentation

Column Extension Procedure

Description

Function which accepts result from bibit, bibit2 or bibit3 and will (re-)apply the column extension procedure. This means if the result already contained extended biclusters that these will be deleted.

Usage

bibit_columnextension(result, matrix, arff_row_col = NULL, BC = NULL,
  extend_columns = "naive", extend_mincol = 1, extend_limitcol = 1,
  extend_noise = 1, extend_contained = FALSE)

Arguments

result

Result from bibit, bibit2 or bibit3.

matrix

The binary input matrix.

arff_row_col

The same file directories (with the same limitations) as given in bibit, bibit2 or bibit3.

BC

A numeric/integer vector of BC's which should be extended. Different behaviour for the 3 types of input results:

bibit

BC directly takes the corresponding biclusters from the result and extends them. (e.g. BC=c(1,10) is then remapped to c("BC1","BC1_Ext1","BC2","BC2_Ext1") in the new output)

bibit2

BC corresponds with the original non-extended biclusters from the bibit2 result. These original biclusters are selected and extended. (e.g. BC=c(1,10) selects biclusters c("BC1","BC10") which are then remapped to c("BC1","BC1_Ext1","BC2","BC2_Ext1") in the new output)

bibit3

BC corresponds with the biclusters when combining the FULLPATTERN and SUBPATTERN result together. For example choosing BC=1 would only select the 1 FULLPATTERN bicluster for each pattern and try to extend it. (e.g. BC=c(1,10) selects biclusters 1 and 10 from the combined fullpattern and subpattern result (meaning the full pattern BC and the 9th subpattern BC) which are then remapped to c("BC1","BC1_Ext1","BC2","BC2_Ext1") in the new output)

extend_columns

Column Extension Parameter
Can be one of the following: "naive" or "recursive" which will apply either a naive or recursive column extension procedure. (See Details Section for more information.)
Based on the extension, additional biclusters will be created in the Biclust object which can be seen in the column and row names of the RowxNumber and NumberxCol slots ("_Ext" suffix).
The info slot will also contain some additional information. Inside this slot, BC.Extended contains info on which original biclusters were extended, how many columns were added, and in how many extra extended biclusters this resulted.

Warning: Using a percentage-based extend_noise in combination with the recursive procedure will result in a large amount of biclusters and increase the computation time a lot. Depending on the data when using recursive in combination with a noise percentage, it is advised to keep it reasonable small (e.g. 10%). Another remedy is to sufficiently increase the extend_limitcol either as a percentage or integer to limit the candidates of columns.

extend_mincol

Column Extension Parameter
A minimum number of columns that a bicluster should be able to be extended with before saving the result. (Default=1)

extend_limitcol

Column Extension Parameter
The number (extend_limitcol>=1) or percentage (0<extend_limitcol<1) of 1's that a column (subsetted on the BC rows) should at least contain for it to be a candidate to be added to the bicluster as an extension. (Default=1) (Increase this parameter if the recursive extension takes too long. Limiting the pool of candidates will decrease computation time, but restrict the results more.)

extend_noise

Column Extension Parameter
The maximum allowed noise (in each row) when extending the columns of the bicluster. Can take the same as the noise parameter.

extend_contained

Column Extension Parameter
Logical value if extended results should be checked if they contain each other (and deleted if this is the case). Default = FALSE. This can be a lengthy procedure for a large amount of biclusters (>1000).

Value

A Biclust S4 Class object or bibit3 S3 list Class object

Details - Column Extension

An optional procedure which can be applied after applying the BiBit algorithm (with noise) is called Column Extension. The procedure will add extra columns to a BiBit bicluster, keeping into account the allowed extend_noise level in each row. The primary goal is to, after applying BiBit with noise, to also try and add some noise to the 2 initial 'perfect' rows. Other parameters like extend_mincol and extend_limitcol can also further restrict which extensions should be discovered.
This procedure can be done either naively (fast) or recursively (more slow and thorough) with the extend_columns parameter.

"naive"

Subsetting on the bicluster rows, the column candidates are ordered based on the most 1's in a column. Afterwards, in this order, each column is sequentially checked and added when the resulted BC is still within row noise levels.
This has 2 major consequences:

Note that using this method will always result in a maximum of 1 extended bicluster per original bicluster.

"recursive"

Conditioning the group of candidates for the allowed row noise level, each possible/allowed combination of adding columns to the bicluster is checked. Only the resulted biclusters with the highest number of extra columns are saved. Of course this could result in multiple extensions for 1 bicluster if there are multiple 'maximum added columns' results.

Note: These procedures are followed by a fast check if the extensions resulted in any duplicate biclusters. If so, these are deleted from the final result.

Author(s)

Ewoud De Troyer

Examples

## Not run: 

set.seed(1)
data <- matrix(sample(c(0,1),100*100,replace=TRUE,prob=c(0.9,0.1)),nrow=100,ncol=100)
data[1:10,1:10] <- 1 # BC1
data[11:20,11:20] <- 1 # BC2
data[21:30,21:30] <- 1 # BC3
data <- data[sample(1:nrow(data),nrow(data)),sample(1:ncol(data),ncol(data))]

result <- bibit2(data,minr=5,minc=5,noise=0.1,extend_columns = "recursive",
              extend_mincol=1,extend_limitcol=1)
result
result2 <- bibit_columnextension(result=out,matrix=data,arff_row_col=NULL,BC=c(1,10),
                              extend_columns="recursive",extend_mincol=1,
                              extend_limitcol=1,extend_noise=2,extend_contained=FALSE)
result2

## End(Not run)

[Package BiBitR version 0.3.1 Index]