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)