setwd("C:/sepp/work/fabia/experiments")
library(fabia)
library(biclust)
library(truecluster)
library(BicARE)
readPlaidResults <- function(filename,n,l,ab="ab",ss="ss",iter="default") {
require(biclust)
r1 <- readLines(filename)
a1 <- strsplit(r1," ")
la <- length(a1)
p <- as.numeric(a1[[la-4]][1])
if ((p==0)||(la==0)) {
L <- matrix(0,n,1)
Z <- matrix(0,1,l)
p <- 0
} else {
L <- matrix(0,n,p)
Z <- matrix(0,p,l)
j <- 0
r <- 0
for (i in 1:la) {
if (!is.na(a1[[i]][1]))
{
if (a1[[i]][1]=="row")
{
j <- j+1
r <- 1
}
if (a1[[i]][1]=="col")
{
r <- 2
}
if (a1[[i]][1]==as.character(j))
{
if(r==1) {
L[as.numeric(a1[[i]][2]),j] <- 1
}
if(r==2) {
Z[j,as.numeric(a1[[i]][2])] <- 1
}
}
}
}
}
pp<- list()
pp[[1]]="plaid" # method
pp[[2]]=ab # a=alpha(probe) effects; b= beta(conditions) effects
pp[[3]]=ss # seek=ss prefer large, possibly diffuse layers
# seek=ms prefer intense, possibly small layers
pp[[4]]=iter # how many seeking iterations
bicB <- BiclustResult(pp,L,Z,p)
return(bicB)
}
readBicatResults <- function(filename,n,l,method="isa",pre="standardization",tc="2.0",tg="2.0") {
require(biclust)
r1 <- readLines(filename)
a1 <- strsplit(r1," ")
la <- length(a1)
p <- la/3
if ((p==0)||(la==0)) {
L <- matrix(0,n,1)
Z <- matrix(0,1,l)
p <- 0
} else {
L <- matrix(0,n,p)
Z <- matrix(0,p,l)
for (i in 1:p) {
nn <- as.numeric(a1[[3*i-2]][1])
nl <- as.numeric(a1[[3*i-2]][2])
for (k in 1:nn) {
L[as.numeric(a1[[3*i-1]][k]),i] <- 1
}
for (k in 1:nl) {
Z[i,as.numeric(a1[[3*i]][k])] <- 1
}
}
}
pp<- list()
pp[[1]]=method # method
pp[[2]]=pre # preprocessing: standardization
pp[[3]]=tg # gene score threshold
pp[[4]]=tc # condition score threshold
bicB <- BiclustResult(pp,L,Z,p)
return(bicB)
}
readSambaResults <- function(filename,n,l,pre="standardization",opt="valsp_3ap",over="0.5") {
require(biclust)
r1 <- readLines(filename)
a1 <- strsplit(r1,"\t")
la <- length(a1)
s <- 1
while ((a1[[s]][1]!="[Bicd]")&&(s<=la)) { s <- s+1 }
p <- as.numeric(a1[[s-1]][1])+1
if ((p==0)||(la==0)) {
L <- matrix(0,n,1)
Z <- matrix(0,1,l)
p <- 0
} else {
L <- matrix(0,n,p)
Z <- matrix(0,p,l)
s <- s+1
for (i in s:la) {
if (a1[[i]][2]=="1") {
L[as.numeric(a1[[i]][3]),(as.numeric(a1[[i]][1])+1)] <- 1
}
if (a1[[i]][2]=="0") {
Z[(as.numeric(a1[[i]][1])+1),as.numeric(a1[[i]][3])] <- 1
}
}
}
pp<- list()
pp[[1]]="samba" # method
pp[[2]]=pre # preprocessing: standardization
pp[[3]]=opt # options: valsp_3ap
pp[[4]]=over # overlap genes 0.1 or 0.5
bicB <- BiclustResult(pp,L,Z,p)
return(bicB)
}
indices<- function (bicA, bicB)
{
require(truecluster)
pA <- bicA@Number
pB <- bicB@Number
if ((pA>0)&&(pB>0)) {
n <- length(bicA@RowxNumber[,1])
l <- length(bicA@NumberxCol[1,])
u <- n*l
jamat <- matrix(0,pA,pB)
kumat <- matrix(0,pA,pB)
ocmat <- matrix(0,pA,pB)
somat <- matrix(0,pA,pB)
for (i in 1:pA) {
bcA <- tcrossprod(bicA@RowxNumber[,i],bicA@NumberxCol[i,])
apos <- bcA > 0
sa <- sum(apos)
if (sa > 0.5*u) {
bcA[apos] <- 0
sa <- 0
}
for (j in 1:pB) {
bcB <- tcrossprod(bicB@RowxNumber[,j],bicB@NumberxCol[j,])
bpos <- bcB > 0
sb <- sum(bpos)
if (sb > 0.5*u) {
bcB[bpos] <- 0
sb <- 0
}
bcAB <- bcA + bcB
abpos <- bcAB > 0
sab <- sum(abpos)
if (sab>0) {
jamat[i,j] <- (sa + sb)/sab - 1
somat[i,j] <- 2.0-2.0*sab/(sa+sb)
} else {
jamat[i,j] <- 0
somat[i,j] <- 0
}
if ((sa>0)&&(sb>0))
{
kumat[i,j] <- 1.0+0.5*( (sa-sab)/sb + (sb -sab)/sa )
ocmat[i,j] <- (sa+sb-sab)/sqrt(sb*sa)
}else {
kumat[i,j] <- 0
ocmat[i,j] <- 0
}
}
}
fac <- sqrt(pB*pA)
mm <- min(pA,pB)
ma <- max(pA,pB)
sja <- sum(jamat)/fac
sku <- sum(kumat)/fac
soc <- sum(ocmat)/fac
sso <- sum(somat)/fac
indja <- munkres(-jamat,tieorder = FALSE)
indku <- munkres(-kumat,tieorder = FALSE)
indoc <- munkres(-ocmat,tieorder = FALSE)
indso <- munkres(-somat,tieorder = FALSE)
rjat <- sum(diag(jamat[indja$row, indja$col]))
rkut <- sum(diag(kumat[indku$row, indku$col]))
roct <- sum(diag(ocmat[indoc$row, indoc$col]))
rsot <- sum(diag(somat[indso$row, indso$col]))
rja <- rjat/mm
rku <- rkut/mm
roc <- roct/mm
rso <- rsot/mm
rja1 <- rjat/ma
rku1 <- rkut/ma
roc1 <- roct/ma
rso1 <- rsot/ma
} else {
rja <- 0
rku <- 0
roc <- 0
rso <- 0
rja1 <- 0
rku1 <- 0
roc1 <- 0
rso1 <- 0
sja <- 0
sku <- 0
soc <- 0
sso <- 0
}
return(as.vector(c(rja,rku,roc,rso,rja1,rku1,roc1,rso1,sja,sku,soc,sso)))
}
convertFabia <- function(rFab,n=1000,l=100,minc=5,minr=30,method="fabia",cyc=200,alpha=0.3,spl=1.0,spz=1.0,p=13,sL=0.0,sZ=0.0,La=NULL,Za=NULL,lapla=NULL,Psi=NULL)
{
require(biclust)
p <- length(rFab$bic[,1])
pp <- 0
for (i in 1:p) {
if (rFab$bic[i,1]$binp[1]>=minr)
{
if (rFab$bic[i,1]$binp[2]>=minc) {
pp <- pp + 1
}
}
}
if ((p==0)||(pp==0)) {
L <- matrix(0,n,1)
Z <- matrix(0,1,l)
pp <- 0
} else {
L <- matrix(0,n,pp)
Z <- matrix(0,pp,l)
j <- 0
for (i in 1:p) {
if (rFab$bic[i,1]$binp[1]>=minr)
{
if (rFab$bic[i,1]$binp[2]>=minc) {
j <- j + 1
for (k in 1:rFab$bic[i,1]$binp[2]) {
Z[j,rFab$num[i,2]$numnp[k]] <- 1
}
for (k in 1:rFab$bic[i,1]$binp[1]) {
L[rFab$num[i,1]$numng[k],j] <- 1
}
}
}
}
}
lp<- list()
lp[[1]]=method
lp[[2]]=cyc
lp[[3]]=alpha
lp[[4]]=spl
lp[[5]]=spz
lp[[6]]=p
lp[[7]]=sL
lp[[8]]=sZ
lp[[9]]=La
lp[[10]]=Za
lp[[11]]=lapla
lp[[12]]=Psi
bicB <- BiclustResult(lp,L,Z,pp)
return(bicB)
}
convertDat <- function(dat,n=1000,l=100)
{
require(biclust)
p <- length(dat$LC)
L <- matrix(0,n,p)
Z <- matrix(0,p,l)
for (i in 1:p) {
for (k in 1:length(dat$LC[[i]])) {
L[dat$LC[[i]][k],i] <- 1
}
for (k in 1:length(dat$ZC[[i]])) {
Z[i,dat$ZC[[i]][k]] <- 1
}
}
lp<- list()
lp[[1]]="make_fabi_data"
lp[[2]]=n
lp[[3]]=l
bicB <- BiclustResult(lp,L,Z,p)
return(bicB)
}
indrorig_s<-list()
indrfabia_s<-list()
indrfabias_s<-list()
indrfabiap_s<-list()
indrmfsc_s<-list()
indrplaid_ss_s<-list()
indrplaid_ms_s<-list()
indrplaid_ms_5_s<-list()
indrisa_s<-list()
indrisa_1_s<-list()
indropsm_s<-list()
indrsamba_s<-list()
indrxmotif_s<-list()
indrbimax_s<-list()
indrcc_s<-list()
indrplaid_t_ab_s<-list()
indrplaid_t_a_s<-list()
indrspec_s<-list()
indrfloc_s<-list()
sindrorig_s<- as.vector(rep(0,12))
sindrfabia_s<- as.vector(rep(0,12))
sindrfabias_s<- as.vector(rep(0,12))
sindrfabiap_s<- as.vector(rep(0,12))
sindrmfsc_s<- as.vector(rep(0,12))
sindrplaid_ss_s<- as.vector(rep(0,12))
sindrplaid_ms_s<- as.vector(rep(0,12))
sindrplaid_ms_5_s<- as.vector(rep(0,12))
sindrisa_s<- as.vector(rep(0,12))
sindrisa_1_s<- as.vector(rep(0,12))
sindropsm_s<- as.vector(rep(0,12))
sindrsamba_s<- as.vector(rep(0,12))
sindrxmotif_s<- as.vector(rep(0,12))
sindrbimax_s<- as.vector(rep(0,12))
sindrcc_s<- as.vector(rep(0,12))
sindrplaid_t_ab_s<- as.vector(rep(0,12))
sindrplaid_t_a_s<- as.vector(rep(0,12))
sindrspec_s<- as.vector(rep(0,12))
sindrfloc_s<- as.vector(rep(0,12))
#=====================================================================
#=====================================================================
m <- 100
n=1000
l=100
alpha_fabia = 0.4
alpha_fabias = 0.6
spl=1.0
spz=1.0
cyc=200
p=13
#=====================================================================
#=====================================================================
for (i in 1:m) {
load(file=paste("exp_",as.character(i),".RData",sep = ""))
rorig <- convertDat(dat,n=1000,l=100)
save(rorig,file=paste("exp_",as.character(i),"_Biclust_orig.RData",sep = ""))
X <- dat[[1]]
X <- X- rowMeans(X)
XX <- (1/ncol(X))*tcrossprod(X)
dXX <- 1/sqrt(diag(XX)+0.001*as.vector(rep(1,nrow(X))))
X <- dXX*X
resFab <- fabia(X,cyc,alpha_fabia,spl,spz,p)
rFab <- extract_bic(resFab$L,resFab$Z,lapla=resFab$lapla,Psi=resFab$Psi)
rfabia <- convertFabia(rFab,n=n,l=l,minc=5,minr=30,method="fabia",cyc=cyc,alpha=alpha_fabia,spl=spl,spz=spz,p=p,sL=0.0,sZ=0.0,L=resFab$L,Z=resFab$Z,lapla=resFab$lapla,Psi=resFab$Psi)
save(rfabia,file=paste("exp_",as.character(i),"_Biclust_fabia.RData",sep = ""))
resFab <- fabias(X,cyc,alpha_fabias,spz,p)
rFab <- extract_bic(resFab$L,resFab$Z,lapla=resFab$lapla,Psi=resFab$Psi)
rfabias <- convertFabia(rFab,n=n,l=l,minc=5,minr=30,method="fabias",cyc=cyc,alpha=alpha_fabias,spl=0,spz=spz,p=p,sL=0.0,sZ=0.0,L=resFab$L,Z=resFab$Z,lapla=resFab$lapla,Psi=resFab$Psi)
save(rfabias,file=paste("exp_",as.character(i),"_Biclust_fabias.RData",sep = ""))
resFab <- fabiap(X,cyc,alpha_fabia,spl,spz,13,alpha_fabias,alpha_fabias)
rFab <- extract_bic(resFab$L,resFab$Z,lapla=resFab$lapla,Psi=resFab$Psi)
rfabiap <- convertFabia(rFab,n=n,l=l,minc=5,minr=30,method="fabiap",cyc=cyc,alpha=alpha_fabia,spl=spl,spz=spz,p=p,sL=alpha_fabias,sZ=alpha_fabias,L=resFab$L,Z=resFab$Z,lapla=resFab$lapla,Psi=resFab$Psi)
save(rfabiap,file=paste("exp_",as.character(i),"_Biclust_fabiap.RData",sep = ""))
resFab <- mfsc(X,p,alpha_fabias,alpha_fabias)
rFab <- extract_bic(resFab$L,resFab$Z)
rmfsc <- convertFabia(rFab,n=1000,l=100,minc=5,minr=30,method="mfsc",cyc=0,alpha=0,spl=0,spz=0,p=p,sL=alpha_fabias,sZ=alpha_fabias,L=resFab$L,Z=resFab$Z,lapla=NULL,Psi=NULL)
save(rmfsc,file=paste("exp_",as.character(i),"_Biclust_mfsc.RData",sep = ""))
rplaid_ss<- readPlaidResults(paste("exp_",as.character(i),"_plaid_ss.res",sep = ""),1000,100,ab="ab",ss="ss",iter="default")
save(rplaid_ss,file=paste("exp_",as.character(i),"_Biclust_plaid_ss.RData",sep = ""))
rplaid_ms<- readPlaidResults(paste("exp_",as.character(i),"_plaid_ms.res",sep = ""),1000,100,ab="ab",ss="ms",iter="default")
save(rplaid_ms,file=paste("exp_",as.character(i),"_Biclust_plaid_ms.RData",sep = ""))
rplaid_ms_5 <- readPlaidResults(paste("exp_",as.character(i),"_plaid_ms_5.res",sep = ""),1000,100,ab="ab",ss="ms",iter="5")
save(rplaid_ms_5,file=paste("exp_",as.character(i),"_Biclust_plaid_ms_5.RData",sep = ""))
risa <- readBicatResults(paste("exp_",as.character(i),"_isa.res",sep = ""),1000,100,method="isa",pre="standardization",tc="2.0",tg="2.0")
save(risa,file=paste("exp_",as.character(i),"_Biclust_isa.RData",sep = ""))
risa_1 <- readBicatResults(paste("exp_",as.character(i),"_isa_1.res",sep = ""),1000,100,method="isa",pre="standardization",tc="1.0",tg="1.0")
save(risa_1,file=paste("exp_",as.character(i),"_Biclust_isa_1.RData",sep = ""))
ropsm <- readBicatResults(paste("exp_",as.character(i),"_opsm.res",sep = ""),1000,100,method="opsm",pre="standardization",tc="",tg="")
save(ropsm,file=paste("exp_",as.character(i),"_Biclust_opsm.RData",sep = ""))
rsamba <- readSambaResults(paste("exp_",as.character(i),"_samba.res",sep = ""),1000,100,pre="standardization",opt="valsp_3ap",over="0.5")
save(rsamba,file=paste("exp_",as.character(i),"_Biclust_samba.RData",sep = ""))
XD<-discretize(X)
rxmotif <- biclust(XD, method=BCXmotifs(), ns=100, nd=100, sd=5, alpha=0.05, number=13)
save(rxmotif,file=paste("exp_",as.character(i),"_Biclust_xmotif.RData",sep = ""))
XB <- binarize(X)
rbimax <- biclust(XB, method=BCBimax(), minr=30, minc=5, number=13)
save(rbimax,file=paste("exp_",as.character(i),"_Biclust_bimax.RData",sep = ""))
rcc <- biclust(X, method=BCCC(), delta=0.03, alpha=1.2, number=13)
save(rcc,file=paste("exp_",as.character(i),"_Biclust_cc.RData",sep = ""))
rplaid_t_ab <- biclust(X, method=BCPlaid(), cluster="b", fit.model = y ~ m + a + b, background = TRUE, row.release = 0.7, col.release = 0.7,shuffle = 3, back.fit = 0, max.layers = 13, iter.startup = 5, iter.layer = 10, verbose = TRUE)
save(rplaid_t_ab,file=paste("exp_",as.character(i),"_Biclust_plaid_t_ab.RData",sep = ""))
rplaid_t_a <- biclust(X, method=BCPlaid(), cluster="b", fit.model = y ~ m + a, background = TRUE, row.release = 0.7, col.release = 0.7,shuffle = 3, back.fit = 0, max.layers = 13,iter.startup = 5, iter.layer = 10, verbose = TRUE)
save(rplaid_t_a,file=paste("exp_",as.character(i),"_Biclust_plaid_t_a.RData",sep = ""))
rspec <- biclust(exp(X), method=BCSpectral(), normalization="log", numberOfEigenvalues=6, minr=30, minc=5, withinVar=1)
save(rspec,file=paste("exp_",as.character(i),"_Biclust_spec.RData",sep = ""))
resfloc <- FLOC(X, k = 13, pGene = 0.1, pSample=0.1, N = 30, M = 5, t = 500)
rfloc <- BiclustResult(as.list(resfloc$param),t(resfloc$bicRow),resfloc$bicCol,as.numeric(resfloc$param[1,2]))
save(rfloc,file=paste("exp_",as.character(i),"_Biclust_floc.RData",sep = ""))
indrfabia<-indices(rorig,rfabia)
indrfabias<-indices(rorig,rfabias)
indrfabiap<-indices(rorig,rfabiap)
indrmfsc<-indices(rorig,rmfsc)
indrplaid_ss<-indices(rorig,rplaid_ss)
indrplaid_ms<-indices(rorig,rplaid_ms)
indrplaid_ms_5<-indices(rorig,rplaid_ms_5)
indrisa<-indices(rorig,risa)
indrisa_1<-indices(rorig,risa_1)
indropsm<-indices(rorig,ropsm)
indrsamba<-indices(rorig,rsamba)
indrxmotif<-indices(rorig,rxmotif)
indrbimax<-indices(rorig,rbimax)
indrcc<-indices(rorig,rcc)
indrplaid_t_ab<-indices(rorig,rplaid_t_ab)
indrplaid_t_a<-indices(rorig,rplaid_t_a)
indrspec<-indices(rorig,rspec)
indrfloc<-indices(rorig,rfloc)
save(indrfabia,indrfabias,indrfabiap,indrmfsc,indrplaid_ss,indrplaid_ms,indrplaid_ms_5,indrisa,indrisa_1,indropsm,indrsamba,indrxmotif,indrbimax,indrcc,indrplaid_t_ab,indrplaid_t_a,indrspec,indrfloc,file=paste("exp_",as.character(i),"_ind_res.RData",sep = ""))
write.table(t(as.vector(indrfabia)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =FALSE)
write.table(t(as.vector(indrfabias)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrfabiap)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrmfsc)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrplaid_ss)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrplaid_ms)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrplaid_ms_5)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrisa)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrisa_1)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indropsm)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrsamba)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrxmotif)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrbimax)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrcc)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrplaid_t_ab)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrplaid_t_a)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrspec)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(indrfloc)), file = paste("exp_",as.character(i),"_in_res.txt",sep = ""), quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
indrfabia_s[[i]]<-indrfabia
indrfabias_s[[i]]<-indrfabias
indrfabiap_s[[i]]<-indrfabiap
indrmfsc_s[[i]]<-indrmfsc
indrplaid_ss_s[[i]]<-indrplaid_ss
indrplaid_ms_s[[i]]<-indrplaid_ms
indrplaid_ms_5_s[[i]]<-indrplaid_ms_5
indrisa_s[[i]]<-indrisa
indrisa_1_s[[i]]<-indrisa_1
indropsm_s[[i]]<-indropsm
indrsamba_s[[i]]<-indrsamba
indrxmotif_s[[i]]<-indrxmotif
indrbimax_s[[i]]<-indrbimax
indrcc_s[[i]]<-indrcc
indrplaid_t_ab_s[[i]]<-indrplaid_t_ab
indrplaid_t_a_s[[i]]<-indrplaid_t_a
indrspec_s[[i]]<-indrspec
indrfloc_s[[i]]<-indrfloc
sindrfabia_s<-sindrfabia_s + indrfabia
sindrfabias_s<- sindrfabias_s + indrfabias
sindrfabiap_s<-sindrfabiap_s + indrfabiap
sindrmfsc_s<- sindrmfsc_s + indrmfsc
sindrplaid_ss_s<- sindrplaid_ss_s + indrplaid_ss
sindrplaid_ms_s<- sindrplaid_ms_s + indrplaid_ms
sindrplaid_ms_5_s<-sindrplaid_ms_5_s + indrplaid_ms_5
sindrisa_s<- sindrisa_s + indrisa
sindrisa_1_s<-sindrisa_1_s + indrisa_1
sindropsm_s<- sindropsm_s + indropsm
sindrsamba_s<-sindrsamba_s + indrsamba
sindrxmotif_s<-sindrxmotif_s + indrxmotif
sindrbimax_s<- sindrbimax_s + indrbimax
sindrcc_s<- sindrcc_s + indrcc
sindrplaid_t_ab_s<-sindrplaid_t_ab_s + indrplaid_t_ab
sindrplaid_t_a_s<- sindrplaid_t_a_s + indrplaid_t_a
sindrspec_s<- sindrspec_s + indrspec
sindrfloc_s<- sindrfloc_s + indrfloc
rm(dat)
rm(X)
rm(XD)
rm(XB)
rm(XX)
}
sindrfabia_s<-sindrfabia_s/m
sindrfabias_s<- sindrfabias_s/m
sindrfabiap_s<-sindrfabiap_s/m
sindrmfsc_s<- sindrmfsc_s/m
sindrplaid_ss_s<- sindrplaid_ss_s/m
sindrplaid_ms_s<- sindrplaid_ms_s/m
sindrplaid_ms_5_s<-sindrplaid_ms_5_s/m
sindrisa_s<- sindrisa_s/m
sindrisa_1_s<-sindrisa_1_s/m
sindropsm_s<- sindropsm_s/m
sindrsamba_s<-sindrsamba_s/m
sindrxmotif_s<-sindrxmotif_s/m
sindrbimax_s<- sindrbimax_s/m
sindrcc_s<- sindrcc_s/m
sindrplaid_t_ab_s<-sindrplaid_t_ab_s/m
sindrplaid_t_a_s<- sindrplaid_t_a_s/m
sindrspec_s<- sindrspec_s/m
sindrfloc_s<- sindrfloc_s/m
sindrfabia_v<- as.vector(rep(0,12))
sindrfabias_v<- as.vector(rep(0,12))
sindrfabiap_v<- as.vector(rep(0,12))
sindrmfsc_v<- as.vector(rep(0,12))
sindrplaid_ss_v<- as.vector(rep(0,12))
sindrplaid_ms_v<- as.vector(rep(0,12))
sindrplaid_ms_5_v<- as.vector(rep(0,12))
sindrisa_v<- as.vector(rep(0,12))
sindrisa_1_v<- as.vector(rep(0,12))
sindropsm_v<- as.vector(rep(0,12))
sindrsamba_v<- as.vector(rep(0,12))
sindrxmotif_v<- as.vector(rep(0,12))
sindrbimax_v<- as.vector(rep(0,12))
sindrcc_v<- as.vector(rep(0,12))
sindrplaid_t_ab_v<- as.vector(rep(0,12))
sindrplaid_t_a_v<- as.vector(rep(0,12))
sindrspec_v<- as.vector(rep(0,12))
sindrfloc_v<- as.vector(rep(0,12))
for (i in 1:m) {
sindrfabia_v<-(indrfabia_s[[i]]-sindrfabia_s)^2
sindrfabias_v<-(indrfabias_s[[i]]-sindrfabias_s)^2
sindrfabiap_v<-(indrfabiap_s[[i]]-sindrfabiap_s)^2
sindrmfsc_v<-(indrmfsc_s[[i]]-sindrmfsc_s)^2
sindrplaid_ss_v<-(indrplaid_ss_s[[i]]-sindrplaid_ss_s)^2
sindrplaid_ms_v<-(indrplaid_ms_s[[i]]-sindrplaid_ms_s)^2
sindrplaid_ms_5_v<-(indrplaid_ms_5_s[[i]]-sindrplaid_ms_5_s)^2
sindrisa_v<-(indrisa_s[[i]]-sindrisa_s)^2
sindrisa_1_v<-(indrisa_1_s[[i]]-sindrisa_1_s)^2
sindropsm_v<-(indropsm_s[[i]]-sindropsm_s)^2
sindrsamba_v<-(indrsamba_s[[i]]-sindrsamba_s)^2
sindrxmotif_v<-(indrxmotif_s[[i]]-sindrxmotif_s)^2
sindrbimax_v<-(indrbimax_s[[i]]-sindrbimax_s)^2
sindrcc_v<-(indrcc_s[[i]]-sindrcc_s)^2
sindrplaid_t_ab_v<-(indrplaid_t_ab_s[[i]]-sindrplaid_t_ab_s)^2
sindrplaid_t_a_v<-(indrplaid_t_a_s[[i]]-sindrplaid_t_a_s)^2
sindrspec_v<-(indrspec_s[[i]]-sindrspec_s)^2
sindrfloc_v<-(indrfloc_s[[i]]-sindrfloc_s)^2
}
sindrfabia_v<-sindrfabia_v/(m-1)
sindrfabias_v<- sindrfabias_v/(m-1)
sindrfabiap_v<-sindrfabiap_v/(m-1)
sindrmfsc_v<- sindrmfsc_v/(m-1)
sindrplaid_ss_v<- sindrplaid_ss_v/(m-1)
sindrplaid_ms_v<- sindrplaid_ms_v/(m-1)
sindrplaid_ms_5_v<-sindrplaid_ms_5_v/(m-1)
sindrisa_v<- sindrisa_v/(m-1)
sindrisa_1_v<-sindrisa_1_v/(m-1)
sindropsm_v<- sindropsm_v/(m-1)
sindrsamba_v<-sindrsamba_v/(m-1)
sindrxmotif_v<-sindrxmotif_v/(m-1)
sindrbimax_v<- sindrbimax_v/(m-1)
sindrcc_v<- sindrcc_v/(m-1)
sindrplaid_t_ab_v<-sindrplaid_t_ab_v/(m-1)
sindrplaid_t_a_v<- sindrplaid_t_a_v/(m-1)
sindrspec_v<- sindrspec_v/(m-1)
sindrfloc_v<- sindrfloc_v/(m-1)
write.table(t(as.vector(sindrfabia_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =FALSE)
write.table(t(as.vector(sindrfabias_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrfabiap_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrmfsc_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_ss_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_ms_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_ms_5_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrisa_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrisa_1_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindropsm_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrsamba_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrxmotif_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrbimax_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrcc_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_t_ab_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_t_a_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrspec_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrfloc_s)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrfabia_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrfabias_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrfabiap_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrmfsc_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_ss_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_ms_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_ms_5_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrisa_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrisa_1_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindropsm_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrsamba_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrxmotif_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrbimax_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrcc_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_t_ab_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrplaid_t_a_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrspec_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)
write.table(t(as.vector(sindrfloc_v)), file ="final_result.txt", quote = FALSE, sep = "\t",row.names = FALSE,col.names = FALSE,append =TRUE)