XSim.mod: Bi-clustering using Co-Similarity width modification

In daosang/PDI2015: Bi-clustering Biological Dataset using Co-similarity

Description

A modification of co-similarity by Hussain for Gene Expression Data ( See in the reference)

Usage

XSim.mod(x, y, itr = 4)

Arguments

x	matrix or dataframe of predictors, of dimension n*p; each row is an observation vector.
y	response variable (1 or 2)
itr	number of iterations.

Value

Return a list of objects.

References

Hussain S.F. Bi-Clustering Gene Expression Data Using Co-Similarity, 7th International Conference on Advanced Data Mining and Applications (ADMA), 16-19th Dec. 2011, Beijing, China.

Examples

library(PDI2015)
XSim.mod(ColonCancer[, -1], ColonCancer[,1], itr = 4)

#' # Exemple2: Lung Cancer (Gordon et al.2002)
tmp = gordon$x
idx = c()
dem = 1
for (i in 1:dim(tmp)[2]) {
 if (  (abs(max(tmp[,i])/min(tmp[,i])) < 5) || (abs(max(tmp[,i]) - min(tmp[,i])) < 600)) {
   idx[dem] = i
   dem = dem + 1
 }
}

tmp2 = tmp[,-idx]
dim(tmp2)

classs = as.numeric(gordon$y)

# Test 4 algo:
# 1 .XSIM 2008
tt1 = c()
for (i in 1:4){
 tmp = XSim2008(tmp2, classs, itr = i)
 tt1[i] = tmp$accuracy
}

# 4. XSIM.mod of Hussain
tt4 = c()
for (i in 1:4) {
 tmp = XSim.mod(tmp2, classs, itr = i)
 tt4[i] = tmp$accuracy
}

# Comparaison
max(tt1)
max(tt4)
# Exemple 3: Colon Cancer (Alon et al.1999):
tmp = projectPDI2015::ColonCancer[,-1]
idx = c()
dem = 1
for (i in 1:dim(tmp)[2]) {
 if (  (abs(max(tmp[,i])/min(tmp[,i])) < 15) || (abs(max(tmp[,i]) - min(tmp[,i])) < 500)) {
  idx[dem] = i
  dem = dem + 1
}
}

tmp2 = tmp[,-idx]
dim(tmp2)


# Test 4 algo:
# 1 .XSIM 2008
tt1 = c()
for (i in 1:4){
tmp = XSim2008(tmp2, ColonCancer[,1], itr = i)
tt1[i] = tmp$accuracy
}

# 2. XSIM 2010
tt2 = c()
for (i in 1:4){
tmp = XSim2010(tmp2, ColonCancer[,1], itr = i)
tt2[i] = tmp$accuracy
}

# 3. XSIM 2015
tt3 = c()
for (i in 1:4){
tmp = XSim2015(tmp2, ColonCancer[,1], itr = i)
 tt3[i] = tmp$accuracy
}

# 4. XSIM.mod of Hussain
tt4 = c()
for (i in 1:4) {
 tmp = XSim.mod(tmp2, ColonCancer[,1], itr = i)
 tt4[i] = tmp$accuracy
}

# Comparaison
max(tt1)
# max(tt2)
max(tt3)
max(tt4)

daosang/PDI2015 documentation built on May 14, 2019, 6:07 p.m.