CompareResultJI: Compare Biclustering Results using Jaccard Index

In 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)

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).

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)

BiBitR documentation built on May 2, 2019, 4:18 a.m.