CompareResultJI: Compare Biclustering Results using Jaccard Index

In ewouddt/BiBitR: R Wrapper for Java Implementation of BiBit

Description

Creates a heatmap and returns a similarity matrix of the Jaccard Index (Row, Column or both dimensions) in order to compare 2 different biclustering results or compare the biclusters of a single result.

Usage

CompareResultJI(BCresult1, BCresult2 = NULL, type = "both", plot = TRUE,
  MultiCores = FALSE, MultiCores.number = detectCores(logical = FALSE))

Arguments

BCresult1	A S4 Biclust object. If only this input Biclust object is given, the biclusters of this single result will be compared.
BCresult2	A second S4 Biclust object to which BCresult1 should be compared. (default=NULL)
type	Of which dimension should the Jaccard Index be computed? Can be "row", "col" or "both" (default).
plot	Logical value if plot should be outputted (default=TRUE).
MultiCores	Logical value parallelisation should be used to compute the JI similarity matrix (advantageous for more than approximately 1500 Biclusters). FALSE by default.
MultiCores.number	Number of cores to be used for MultiCores=TRUE. By default total number of physical cores.

Details

The Jaccard Index between two biclusters is calculated as following:

JI(BC1,BC2) = \frac{(m_1+m_2-m_{12})}{m_{12}}

in which

• type="row" or type="col"

  • m_1= Number of rows/columns of BC1

  • m_2= Number of rows/columns of BC2

  • m_{12}= Number of rows/columns of union of row/column membership of BC1 and BC2

• type="both"

  • m_1= Size of BC1 (rows times columns)

  • m_2= Size of BC2 (rows times columns)

  • m_{12}= m_1+m_2 - size of overlapping BC of BC1 and BC2

Value

A list containing

• SimMat: The JI Similarity Matrix between the compared biclusters.

• MaxSim: A list containing the maximum values on each row (BCResult1) and each column (BCResult2).

Author(s)

Ewoud De Troyer

Examples

## 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 1
result1 <- bibit(data,minr=5,minc=5)
result1

# Result 2
result2 <- bibit(data,minr=2,minc=2)
result2

## Compare all BC's of Result 1 ##
Sim1 <- CompareResultJI(BCresult1=result1,type="both")
Sim1$SimMat

## Compare BC's of Result 1 and 2 ##
Sim12 <- CompareResultJI(BCresult1=result1,BCresult2=result2,type="both",plot=FALSE)
str(Sim12)

## End(Not run)

ewouddt/BiBitR documentation built on May 16, 2019, 9:41 a.m.