A Rwrapper which directly calls the original Java code for the BiBit algorithm (http://eps.upo.es/bigs/BiBit.html) and transforms it to the output format of the Biclust
R package.
1 2 
matrix 
The binary input matrix. 
minr 
The minimum number of rows of the Biclusters. 
minc 
The minimum number of columns of the Biclusters. 
arff_row_col 
If you want to circumvent the internal R function to convert the matrix to 
output_path 
If as output, the original txt output of the Java code is desired, provide the outputh path here (without extension). In this case the 
This function uses the original Java code directly (with the intended input and output). Because the Java code was not refactored, the rJava
package could not be used.
The bibit
function does the following:
Convert R matrix to a .arff
output file.
Use the .arff
file as input for the Java code which is called by system()
.
The outputted .txt
file from the Java BiBit algorithm is read in and transformed to a Biclust
object.
Because of this, there is a chance of overhead when applying the algorithm on large datasets. Make sure your machine has enough RAM available when applying to big data.
A Biclust S4 Class object.
Ewoud De Troyer
Domingo S. RodriguezBaena, Antonia J. PerezPulido and Jesus S. AguilarRuiz (2011), "A biclustering algorithm for extracting bitpatterns from binary datasets", Bioinformatics
1 2 3 4 5 6 7 8 9 10  ## Not run:
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 < bibit(data,minr=5,minc=5)
result
## End(Not run)

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