GSReg_Kendall: Calculate Kendall-tau distance in different forms

In FertigLab/GSReg: Gene Set Regulation (GS-Reg)

Description

Different types of calculations of kendall-tau distance.

Usage

GSReg.kendall.tau.distance(V)
GSReg.kendall.tau.distance.template(V, Temp)
GSReg.kendall.tau.distance.restricted(V, RestMat)

Arguments

V	A matrix on which the distances will be calculated. The distance will be calculated between any pair of columns
Temp	A square binary template matrix, like DIRAC template, whose columns and rows correspond to the rows of V. In general, Temp provides a template for comparisons in V. Temp[i,j]==1 means that the template expects that V[i,.]<V[j,.] and 0 means the reverse.
RestMat	Restricted matrix. It must be a square matrix and symmetric with binary 0 or 1 whose columns and rows correspond to the rows of V. Only comparisons with one will be considered.

Details

GSReg.kendall.tau.distance returns kendall-tau calculates distance matrix between any pair of columns of V.

GSReg.kendall.tau.distance.template returns kendall-tau calculates distance matrix between any column V and a template. Temp[i,j] represent a comaprison between the i-th and j-th element of a vector. Hence, the out come's k-th element is (V[i,k]<V[j,k] & RestMat[i,j]==1)/((nrow(RestMat)*(nrow(RestMat)-1))/2).

GSReg.kendall.tau.distance.restricted calculates the Kendall-tau distance and the only considered comparisons are those RestMat[i,j]==1. It is a modified Kendall-tau distance used by SEVA.

Value

Kendall-tau distance.

Author(s)

Bahman Afsari

See Also

GSReg.GeneSets.DIRAC,GSReg.GeneSets.EVA

Examples

library(GSReg)
V <- cbind(c(1,5,3),c(3,2,1))
rownames(V) <- c("F1","F2","F3")
colnames(V) <- c("S1","S2")


myRest1 <- cbind(c(0,1,1),c(1,0,1),c(1,1,0))
rownames(myRest1) <- rownames(V) 
colnames(myRest1) <- rownames(V) 

GSReg.kendall.tau.distance.restricted(V,myRest1)

GSReg.kendall.tau.distance(V)

myRest2 <- cbind(c(0,0,1),c(0,0,1),c(1,1,0))
rownames(myRest2) <- rownames(V) 
colnames(myRest2) <- rownames(V) 
GSReg.kendall.tau.distance.restricted(V,myRest2)


Temp1 <- cbind(c(0,1,1),c(0,0,0),c(0,1,0))
rownames(Temp1) <- rownames(V)
colnames(Temp1) <- rownames(V)

GSReg.kendall.tau.distance.template(V,Temp = Temp1)

FertigLab/GSReg documentation built on May 3, 2021, 6:51 p.m.