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R/exportResultLPSolve.R
In CARNIVAL: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Defines functions
exportResultLPSolve
## Extract and export the optimisation results from the cplex solution file
## (XML) as files and variables for further plotting functions - lpSolve
##
## Enio gjerga, 2020
exportResultLPSolve <- function(variables = variables,
conditionIDX = conditionIDX,
pknList = pknList, inputs=inputs,
measurements=measurements,
lpSolution=lpSolution, mt=mt){
solMatrix <- mt
solMatrix[, 2] <- lpSolution
colnames(solMatrix) <- c("name", "var")
solMatrix <- as.data.frame(solMatrix)
solMatrix$name <- as.character(solMatrix$name)
solMatrix$var <- as.character(solMatrix$var)
vars <- solMatrix$name
sifAll <- list()
nodesAll <- list()
nodesActAll <- list()
idxNodes <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxNodes])
idxNodesUp <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxNodesUp])
idxNodesDown <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxNodesDown])
idxEdgesUp <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxEdgesUp])
idxEdgesDown <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxEdgesDown])
indeces <- c(idxNodes, idxNodesUp, idxNodesDown, idxEdgesUp, idxEdgesDown)
solMatrix = as.matrix(solMatrix)
for(ii in seq(from = 2, to = ncol(solMatrix), by = 1)){
values <- solMatrix[, ii]
valNodes <- as.numeric(values[idxNodes])
valNodesDown <- as.numeric(values[idxNodesDown])
valNodesUp <- as.numeric(values[idxNodesUp])
valEdgesUp <- as.numeric(values[idxEdgesUp])
valEdgesDown <- as.numeric(values[idxEdgesDown])
nodes <- matrix(data = "", nrow = length(idxNodes), ncol = 2)
nodesUp <- matrix(data = "", nrow = length(idxNodesUp), ncol = 2)
nodesDown <- matrix(data = "", nrow = length(idxNodesDown), ncol = 2)
edgesUp <- matrix(data = "", nrow = length(idxEdgesUp), ncol = 2)
edgesDown <- matrix(data = "", nrow = length(idxEdgesDown), ncol = 2)
ctrl <- 0
colnames(nodes) <- c("variable", "value")
colnames(nodesUp) <- c("variable", "value")
colnames(nodesDown) <- c("variable", "value")
colnames(edgesUp) <- c("variable", "value")
colnames(edgesDown) <- c("variable", "value")
nodes[, 1] <- vars[idxNodes]
nodes[, 2] <- as.numeric(values[idxNodes])
# nodes[which(nodes[, 2]>0), 2] <- 1
nodesUp[, 1] <- vars[idxNodesUp]
nodesUp[, 2] <- as.numeric(values[idxNodesUp])
# nodesUp[which(nodesUp[, 2]>0), 2] <- 1
nodesDown[, 1] <- vars[idxNodesDown]
nodesDown[, 2] <- as.numeric(values[idxNodesDown])
# nodesDown[which(nodesDown[, 2]>0), 2] <- 1
edgesUp[, 1] <- vars[idxEdgesUp]
edgesUp[, 2] <- as.numeric(values[idxEdgesUp])
# edgesUp[which(edgesUp[, 2]>0), 2] <- 1
edgesDown[, 1] <- vars[idxEdgesDown]
edgesDown[, 2] <- as.numeric(values[idxEdgesDown])
# edgesDown[which(edgesDown[, 2]>0), 2] <- 1
nodes <- matrix(data = "", nrow = length(idxNodes), ncol = 2)
nodesUp <- matrix(data = "", nrow = length(idxNodesUp), ncol = 2)
nodesDown <- matrix(data = "", nrow = length(idxNodesDown), ncol = 2)
edgesUp <- matrix(data = "", nrow = length(idxEdgesUp), ncol = 2)
edgesDown <- matrix(data = "", nrow = length(idxEdgesDown), ncol = 2)
ctrl <- 0
colnames(nodes) <- c("variable", "value")
colnames(nodesUp) <- c("variable", "value")
colnames(nodesDown) <- c("variable", "value")
colnames(edgesUp) <- c("variable", "value")
colnames(edgesDown) <- c("variable", "value")
nodes[, 1] <- vars[idxNodes]
nodes[, 2] <- as.numeric(values[idxNodes])
nodesUp[, 1] <- vars[idxNodesUp]
nodesUp[, 2] <- as.numeric(values[idxNodesUp])
nodesDown[, 1] <- vars[idxNodesDown]
nodesDown[, 2] <- as.numeric(values[idxNodesDown])
edgesUp[, 1] <- vars[idxEdgesUp]
edgesUp[, 2] <- as.numeric(values[idxEdgesUp])
edgesDown[, 1] <- vars[idxEdgesDown]
edgesDown[, 2] <- as.numeric(values[idxEdgesDown])
if(!is(edgesDown, "matrix")){
edgesDown <- as.matrix(t(edgesDown))
}
if(!is(edgesUp, "matrix")){
edgesUp <- as.matrix(t(edgesUp))
}
# Writing SIF and DOT files
pknList <- as.matrix(pknList)
sif <- matrix(data = "", nrow = 1, ncol = 3)
colnames(sif) <- colnames(pknList)
kk1 <- as.numeric(which(edgesUp[, 2] == 1))
if(length(kk1) > 0){
for(i in seq_len(length(kk1))){
ss <-
strsplit(
strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesUp[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][1]
tt <-
strsplit(
strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesUp[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][2]
if(as.numeric(edgesUp[kk1[i], 2])==as.numeric(
nodesUp[which(
nodesUp[, 1]==variables[[conditionIDX]]$variables[which(
variables[[conditionIDX]]$exp==paste0("SpeciesUP ", tt,
" in experiment ",
conditionIDX))]), 2])){
sif <- rbind(sif, pknList[kk1[i], ])
}
}
}
kk1 <- as.numeric(which(edgesDown[, 2] == 1))
if(length(kk1) > 0){
for(i in seq_len(length(kk1))){
ss <-
strsplit(strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesDown[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][1]
tt <-
strsplit(strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesDown[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][2]
if(as.numeric(edgesDown[kk1[i], 2])==as.numeric(
nodesDown[which(
nodesDown[, 1]==variables[[conditionIDX]]$variables[which(
variables[[conditionIDX]]$exp==paste0("SpeciesDown ", tt,
" in experiment ",
conditionIDX))]), 2])){
sif <- rbind(sif, pknList[kk1[i], ])
}
}
}
if (nrow(sif)==2) {
## If there is only one interaction (plus one empty line)
## convert it to matrix, remove empty line, and convert back to matrix
## for exporting
sif <- as.matrix(sif)
sif <- sif[-1,]
if (is.vector(sif)) {
sif <- t(as.matrix(sif))
}
} else {
sif <- sif[-1,] ## simply remove an empty line
}
if (nrow(sif)==0) {
sif <- NULL
}
## Node activities
nodesAct <- nodes
colnames(nodesAct) <- c("Nodes","Activity")
idx <- intersect(which(nodesAct[, 2] != "0"),
which(nodesAct[, 2] != "-0"))
if (length(idx)!=0) {
activityNodes <- matrix(data = , nrow = length(idx), ncol = 2)
activityNodes[, 2] <- nodesAct[idx, 2]
for(i in seq_len(length(idx))){
activityNodes[i, 1] <-
strsplit(variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==nodesAct[idx[i], 1])],
split = " ")[[1]][2]
}
colnames(activityNodes) <- c("Nodes","Activity")
} else if (length(idx)==0) {
activityNodes = "All node activities are 0"
}
sifAll[[length(sifAll)+1]] <- sif
nodesAll[[length(nodesAll)+1]] <- nodes
nodesActAll[[length(nodesActAll)+1]] <- activityNodes
}
if(length(sifAll)==0){
message("No network was generated for this setting..")
RES <- NULL
return(RES)
} else {
for(ii in seq_len(length(sifAll))){
if(ii ==1){
SIF <- sifAll[[ii]]
} else {
SIF <- unique(rbind(SIF, sifAll[[ii]]))
}
}
##
weightedSIF <- matrix(data = , nrow = nrow(SIF), ncol = 4)
weightedSIF[, seq_len(3)] <- SIF
for(i in seq_len(nrow(SIF))){
cnt <- 0
for(j in seq_len(length(sifAll))){
idxNode1 <- which(sifAll[[j]][, 1]==SIF[i, 1])
idxSign <- which(sifAll[[j]][, 2]==SIF[i, 2])
idxNode2 <- which(sifAll[[j]][, 3]==SIF[i, 3])
idx1 <- intersect(idxNode1, idxNode2)
if(length(idx1) > 0){
idx2 <- intersect(idxSign, idx1)
if(length(idx2) > 0){
cnt <- cnt + 1
}
}
}
weightedSIF[i, 4] <- as.character(cnt*100/length(sifAll))
}
colnames(weightedSIF) <- c("Node1", "Sign", "Node2", "Weight")
##
nodesVar <- c()
for(ii in seq_len(length(nodesAll))){
nodesVar <- unique(c(nodesVar, unique(nodesAll[[ii]][, 1])))
}
nodesNames <- c()
var <- variables[[conditionIDX]]
for(ii in seq_len(length(nodesVar))){
nodesNames <- c(nodesNames,
strsplit(x = var$exp[which(
var$variables==nodesVar[ii])], split = " ")[[1]][2])
}
nodesAttributes <- matrix(data = , nrow = length(nodesNames), ncol = 6)
nodesAttributes[, 1] <- nodesNames
for(i in seq_len(nrow(nodesAttributes))){
zeroCnt <- 0
upCnt <- 0
downCnt <- 0
for(j in seq_len(length(nodesAll))){
currVar <- nodesVar[i]
idx <- which(nodesAll[[j]][, 1]==currVar)
if(round(as.numeric(nodesAll[[j]][idx, 2]))==0){
zeroCnt <- zeroCnt + 1
}
if(round(as.numeric(nodesAll[[j]][idx, 2]))==1){
upCnt <- upCnt + 1
}
if(round(as.numeric(nodesAll[[j]][idx, 2]))==-1){
downCnt <- downCnt + 1
}
}
nodesAttributes[i, 2] <- as.character(zeroCnt*100/length(nodesAll))
nodesAttributes[i, 3] <- as.character(upCnt*100/length(nodesAll))
nodesAttributes[i, 4] <- as.character(downCnt*100/length(nodesAll))
nodesAttributes[i, 5] <-
as.character((zeroCnt*0+upCnt*1+downCnt*(-1))*100/length(nodesAll))
if(nodesAttributes[i, 1]%in%colnames(measurements)){
nodesAttributes[i, 6] <- "T"
} else {
if(nodesAttributes[i, 1]%in%colnames(inputs)){
nodesAttributes[i, 6] <- "S"
} else {
nodesAttributes[i, 6] <- ""
}
}
}
colnames(nodesAttributes) <- c("Node", "ZeroAct", "UpAct",
"DownAct", "AvgAct", "NodeType")
RES <- list()
RES[[length(RES)+1]] <- weightedSIF
RES[[length(RES)+1]] <- nodesAttributes
RES[[length(RES)+1]] <- sifAll
RES[[length(RES)+1]] <- nodesActAll
names(RES) <- c("weightedSIF", "nodesAttributes","sifAll","attributesAll")
return(RES)
}
}
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CARNIVAL documentation built on Nov. 8, 2020, 5:24 p.m.
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Defines functions exportResultLPSolve
## Extract and export the optimisation results from the cplex solution file
## (XML) as files and variables for further plotting functions - lpSolve
##
## Enio gjerga, 2020
exportResultLPSolve <- function(variables = variables,
conditionIDX = conditionIDX,
pknList = pknList, inputs=inputs,
measurements=measurements,
lpSolution=lpSolution, mt=mt){
solMatrix <- mt
solMatrix[, 2] <- lpSolution
colnames(solMatrix) <- c("name", "var")
solMatrix <- as.data.frame(solMatrix)
solMatrix$name <- as.character(solMatrix$name)
solMatrix$var <- as.character(solMatrix$var)
vars <- solMatrix$name
sifAll <- list()
nodesAll <- list()
nodesActAll <- list()
idxNodes <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxNodes])
idxNodesUp <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxNodesUp])
idxNodesDown <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxNodesDown])
idxEdgesUp <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxEdgesUp])
idxEdgesDown <-
which(vars%in%variables[[conditionIDX]]$variables[
variables[[conditionIDX]]$idxEdgesDown])
indeces <- c(idxNodes, idxNodesUp, idxNodesDown, idxEdgesUp, idxEdgesDown)
solMatrix = as.matrix(solMatrix)
for(ii in seq(from = 2, to = ncol(solMatrix), by = 1)){
values <- solMatrix[, ii]
valNodes <- as.numeric(values[idxNodes])
valNodesDown <- as.numeric(values[idxNodesDown])
valNodesUp <- as.numeric(values[idxNodesUp])
valEdgesUp <- as.numeric(values[idxEdgesUp])
valEdgesDown <- as.numeric(values[idxEdgesDown])
nodes <- matrix(data = "", nrow = length(idxNodes), ncol = 2)
nodesUp <- matrix(data = "", nrow = length(idxNodesUp), ncol = 2)
nodesDown <- matrix(data = "", nrow = length(idxNodesDown), ncol = 2)
edgesUp <- matrix(data = "", nrow = length(idxEdgesUp), ncol = 2)
edgesDown <- matrix(data = "", nrow = length(idxEdgesDown), ncol = 2)
ctrl <- 0
colnames(nodes) <- c("variable", "value")
colnames(nodesUp) <- c("variable", "value")
colnames(nodesDown) <- c("variable", "value")
colnames(edgesUp) <- c("variable", "value")
colnames(edgesDown) <- c("variable", "value")
nodes[, 1] <- vars[idxNodes]
nodes[, 2] <- as.numeric(values[idxNodes])
# nodes[which(nodes[, 2]>0), 2] <- 1
nodesUp[, 1] <- vars[idxNodesUp]
nodesUp[, 2] <- as.numeric(values[idxNodesUp])
# nodesUp[which(nodesUp[, 2]>0), 2] <- 1
nodesDown[, 1] <- vars[idxNodesDown]
nodesDown[, 2] <- as.numeric(values[idxNodesDown])
# nodesDown[which(nodesDown[, 2]>0), 2] <- 1
edgesUp[, 1] <- vars[idxEdgesUp]
edgesUp[, 2] <- as.numeric(values[idxEdgesUp])
# edgesUp[which(edgesUp[, 2]>0), 2] <- 1
edgesDown[, 1] <- vars[idxEdgesDown]
edgesDown[, 2] <- as.numeric(values[idxEdgesDown])
# edgesDown[which(edgesDown[, 2]>0), 2] <- 1
nodes <- matrix(data = "", nrow = length(idxNodes), ncol = 2)
nodesUp <- matrix(data = "", nrow = length(idxNodesUp), ncol = 2)
nodesDown <- matrix(data = "", nrow = length(idxNodesDown), ncol = 2)
edgesUp <- matrix(data = "", nrow = length(idxEdgesUp), ncol = 2)
edgesDown <- matrix(data = "", nrow = length(idxEdgesDown), ncol = 2)
ctrl <- 0
colnames(nodes) <- c("variable", "value")
colnames(nodesUp) <- c("variable", "value")
colnames(nodesDown) <- c("variable", "value")
colnames(edgesUp) <- c("variable", "value")
colnames(edgesDown) <- c("variable", "value")
nodes[, 1] <- vars[idxNodes]
nodes[, 2] <- as.numeric(values[idxNodes])
nodesUp[, 1] <- vars[idxNodesUp]
nodesUp[, 2] <- as.numeric(values[idxNodesUp])
nodesDown[, 1] <- vars[idxNodesDown]
nodesDown[, 2] <- as.numeric(values[idxNodesDown])
edgesUp[, 1] <- vars[idxEdgesUp]
edgesUp[, 2] <- as.numeric(values[idxEdgesUp])
edgesDown[, 1] <- vars[idxEdgesDown]
edgesDown[, 2] <- as.numeric(values[idxEdgesDown])
if(!is(edgesDown, "matrix")){
edgesDown <- as.matrix(t(edgesDown))
}
if(!is(edgesUp, "matrix")){
edgesUp <- as.matrix(t(edgesUp))
}
# Writing SIF and DOT files
pknList <- as.matrix(pknList)
sif <- matrix(data = "", nrow = 1, ncol = 3)
colnames(sif) <- colnames(pknList)
kk1 <- as.numeric(which(edgesUp[, 2] == 1))
if(length(kk1) > 0){
for(i in seq_len(length(kk1))){
ss <-
strsplit(
strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesUp[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][1]
tt <-
strsplit(
strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesUp[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][2]
if(as.numeric(edgesUp[kk1[i], 2])==as.numeric(
nodesUp[which(
nodesUp[, 1]==variables[[conditionIDX]]$variables[which(
variables[[conditionIDX]]$exp==paste0("SpeciesUP ", tt,
" in experiment ",
conditionIDX))]), 2])){
sif <- rbind(sif, pknList[kk1[i], ])
}
}
}
kk1 <- as.numeric(which(edgesDown[, 2] == 1))
if(length(kk1) > 0){
for(i in seq_len(length(kk1))){
ss <-
strsplit(strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesDown[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][1]
tt <-
strsplit(strsplit(
variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==edgesDown[kk1[i], 1])],
split = " ")[[1]][2], split = "=")[[1]][2]
if(as.numeric(edgesDown[kk1[i], 2])==as.numeric(
nodesDown[which(
nodesDown[, 1]==variables[[conditionIDX]]$variables[which(
variables[[conditionIDX]]$exp==paste0("SpeciesDown ", tt,
" in experiment ",
conditionIDX))]), 2])){
sif <- rbind(sif, pknList[kk1[i], ])
}
}
}
if (nrow(sif)==2) {
## If there is only one interaction (plus one empty line)
## convert it to matrix, remove empty line, and convert back to matrix
## for exporting
sif <- as.matrix(sif)
sif <- sif[-1,]
if (is.vector(sif)) {
sif <- t(as.matrix(sif))
}
} else {
sif <- sif[-1,] ## simply remove an empty line
}
if (nrow(sif)==0) {
sif <- NULL
}
## Node activities
nodesAct <- nodes
colnames(nodesAct) <- c("Nodes","Activity")
idx <- intersect(which(nodesAct[, 2] != "0"),
which(nodesAct[, 2] != "-0"))
if (length(idx)!=0) {
activityNodes <- matrix(data = , nrow = length(idx), ncol = 2)
activityNodes[, 2] <- nodesAct[idx, 2]
for(i in seq_len(length(idx))){
activityNodes[i, 1] <-
strsplit(variables[[conditionIDX]]$exp[which(
variables[[conditionIDX]]$variables==nodesAct[idx[i], 1])],
split = " ")[[1]][2]
}
colnames(activityNodes) <- c("Nodes","Activity")
} else if (length(idx)==0) {
activityNodes = "All node activities are 0"
}
sifAll[[length(sifAll)+1]] <- sif
nodesAll[[length(nodesAll)+1]] <- nodes
nodesActAll[[length(nodesActAll)+1]] <- activityNodes
}
if(length(sifAll)==0){
message("No network was generated for this setting..")
RES <- NULL
return(RES)
} else {
for(ii in seq_len(length(sifAll))){
if(ii ==1){
SIF <- sifAll[[ii]]
} else {
SIF <- unique(rbind(SIF, sifAll[[ii]]))
}
}
##
weightedSIF <- matrix(data = , nrow = nrow(SIF), ncol = 4)
weightedSIF[, seq_len(3)] <- SIF
for(i in seq_len(nrow(SIF))){
cnt <- 0
for(j in seq_len(length(sifAll))){
idxNode1 <- which(sifAll[[j]][, 1]==SIF[i, 1])
idxSign <- which(sifAll[[j]][, 2]==SIF[i, 2])
idxNode2 <- which(sifAll[[j]][, 3]==SIF[i, 3])
idx1 <- intersect(idxNode1, idxNode2)
if(length(idx1) > 0){
idx2 <- intersect(idxSign, idx1)
if(length(idx2) > 0){
cnt <- cnt + 1
}
}
}
weightedSIF[i, 4] <- as.character(cnt*100/length(sifAll))
}
colnames(weightedSIF) <- c("Node1", "Sign", "Node2", "Weight")
##
nodesVar <- c()
for(ii in seq_len(length(nodesAll))){
nodesVar <- unique(c(nodesVar, unique(nodesAll[[ii]][, 1])))
}
nodesNames <- c()
var <- variables[[conditionIDX]]
for(ii in seq_len(length(nodesVar))){
nodesNames <- c(nodesNames,
strsplit(x = var$exp[which(
var$variables==nodesVar[ii])], split = " ")[[1]][2])
}
nodesAttributes <- matrix(data = , nrow = length(nodesNames), ncol = 6)
nodesAttributes[, 1] <- nodesNames
for(i in seq_len(nrow(nodesAttributes))){
zeroCnt <- 0
upCnt <- 0
downCnt <- 0
for(j in seq_len(length(nodesAll))){
currVar <- nodesVar[i]
idx <- which(nodesAll[[j]][, 1]==currVar)
if(round(as.numeric(nodesAll[[j]][idx, 2]))==0){
zeroCnt <- zeroCnt + 1
}
if(round(as.numeric(nodesAll[[j]][idx, 2]))==1){
upCnt <- upCnt + 1
}
if(round(as.numeric(nodesAll[[j]][idx, 2]))==-1){
downCnt <- downCnt + 1
}
}
nodesAttributes[i, 2] <- as.character(zeroCnt*100/length(nodesAll))
nodesAttributes[i, 3] <- as.character(upCnt*100/length(nodesAll))
nodesAttributes[i, 4] <- as.character(downCnt*100/length(nodesAll))
nodesAttributes[i, 5] <-
as.character((zeroCnt*0+upCnt*1+downCnt*(-1))*100/length(nodesAll))
if(nodesAttributes[i, 1]%in%colnames(measurements)){
nodesAttributes[i, 6] <- "T"
} else {
if(nodesAttributes[i, 1]%in%colnames(inputs)){
nodesAttributes[i, 6] <- "S"
} else {
nodesAttributes[i, 6] <- ""
}
}
}
colnames(nodesAttributes) <- c("Node", "ZeroAct", "UpAct",
"DownAct", "AvgAct", "NodeType")
RES <- list()
RES[[length(RES)+1]] <- weightedSIF
RES[[length(RES)+1]] <- nodesAttributes
RES[[length(RES)+1]] <- sifAll
RES[[length(RES)+1]] <- nodesActAll
names(RES) <- c("weightedSIF", "nodesAttributes","sifAll","attributesAll")
return(RES)
}
}
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