################################################################################# ezSGCP
ezSGCP <- function(expData, geneID, annotation_db, semilabel = TRUE,
calib = FALSE, norm = TRUE, tom = TRUE,
saveAdja = FALSE, adjaNameFile = "adjacency.Rdata",
hm = "adjaHeatMap.png",
kopt = NULL, method_k = NULL, f.GO = sum, f.conduct = min,
maxIteration = 1e8, numberStart = 1000, eff.egs = TRUE,
saveOrig = TRUE, n_egvec = 100, sil = FALSE,
dir = c("over", "under"), onto = c("BP", "CC", "MF"),
hgCut = NULL, condTest = TRUE,
cutoff = NULL, percent = 0.10, stp = 0.01,
model = "knn", kn = NULL){
# performs A to Z
if(is.null(geneID) && semilabel == TRUE){
warning("geneIDs are required for semilabeling", call. = FALSE)
message("semilabeling will not performed")
semilabel <- FALSE}
if(is.null(geneID)){
geneID <- paste0(rep("gene", nrow(expData)), seq(1,nrow(expData)))}
if(length(geneID) != nrow(expData)){
stop("number of rows in expData must be the same as the number of genes in geneID")}
if(!is.matrix(expData) && !is.data.frame(expData)){
stop("expData must be either a dataframe or a matrix")}
if(ncol(expData) > nrow(expData)){
warning("number of samples larger than the genes!!! \n Do rows correspond to genes?!"
, call. = FALSE)}
if(!is.null(kopt) && kopt != round(kopt) ){
warning("kopt must be either null or an integer")
message("making k null")
kopt <- NULL}
if(length(setdiff(method_k, c("relativeGap", "secondOrderGap", "additiveGap"))) != 0){
warning("method_k can be either relativeGap, secondOrderGap, or additiveGap",
call. = FALSE)
message("making method to NULL")
method_k <- NULL }
if(!is.numeric(maxIteration) || !is.numeric(numberStart)){
warning("maxIteration and numStart must be numeric and integer")
message("making maxIteration and numberStart to default")
maxIteration <- 1e+8
numberStart <- 1000}
if(all(dir %!in% c("under", "over"))){
warning("dir must be in c(under or over) \n making to default",
call. = FALSE)
dir <- c("over", "under")}
if(length(dir) > 2 ){
warning("dir must be in c(under or over) \n making to default",
call. = FALSE)
dir <- c("over", "under")}
if(all(onto %!in% c("BP", "CC", "MF"))){
warning(" onto must be in BP CC MF \n making to default", call. = FALSE)
onto <- c("BP", "CC", "MF")}
if(length(onto) > 3 ){
warning(" onto must be in BP CC MF \n making to default", call. = FALSE)
onto <- c("BP", "CC", "MF")}
if(!is.null(hgCut) && (hgCut >=1 || hgCut <= 0)){
warning(" not correct hgCutoff value \n making to default", call. = FALSE) }
if(condTest != TRUE && condTest != FALSE){
warning(" condTest must be boolean! \n making to deafult", call. = FALSE)
condTest <- TRUE}
if(percent >= 1 || percent <= 0){
warning("percent must be in (0,1) \n making percent to default",
call. = FALSE)
percent <- 0.10 }
if(stp >= 1 || stp <= 0){
warning("step must be in (0,1) \n making stp to default",
call. = FALSE)
stp <- 0.01 }
if(!is.null(model) && model != "knn" & model != "lr"){
warning("model must be either NULL, knn, or lr \n setting to knn", call. = FALSE)
model <- "knn" }
if(semilabel == TRUE && is.null(annotation_db)){
warning("semilabeling need annotation_db \n semilabeling will not be performed",
call. = FALSE)
message("making semilabel to FALSE")
semilabel <- FALSE}
if(!is.null(semilabel) && semilabel != TRUE && semilabel != FALSE){
warning("semilabel must be either TRUE or FALSE", call. = FALSE)
message("making semilabel to FALSE")
semilabel <- FALSE }
newList <- list()
############################################################################### adjacencyMatrix
message("starting network construction step...")
resAdja <- adjacencyMatrix(expData = expData,
calibration = calib, norm = norm, tom = tom,
saveAdja = saveAdja, adjaNameFile = adjaNameFile,
hm = hm)
############################################################################### clustering
message("starting network clustering step...")
resClus <- clustering(adjaMat = resAdja, geneID = geneID,
annotation_db = annotation_db,
kopt = kopt, method = method_k,
func.GO = f.GO, func.conduct = f.conduct,
maxIter = maxIteration, numStart = numberStart,
eff.egs = eff.egs,
saveOrig = saveOrig, n_egvec = n_egvec, sil = sil)
geneID <- resClus$geneID
if(length(resClus$dropped.indices) > 0){
expData <- expData[-resClus$dropped.indices, ] }
rm(resAdja, expData)
newList <- c(newList, setNames(list(resClus), "clustering"))
############################################################################### geneOntology
if(!semilabel){
clusterLabels <- data.frame(geneID = resClus$geneID,
initialClusters = resClus$clusterLabels)
newList <- c(setNames(list(clusterLabels), "clusterLabels"), newList)
}else{
message("starting initial gene ontology enrichment step...")
resGO <- geneOntology(geneUniv = geneID, clusLab = resClus$clusterLabels,
annotation_db = annotation_db,
direction = dir, ontology = onto, hgCutoff = hgCut,
cond = condTest)
newList <- c(newList, setNames(list(resGO), "initial.GO" ))
############################################################################### semiLabeling
message("starting semi-labeling stage...")
resSL <- semiLabeling(geneID = geneID, df_GO = resGO$GOresults,
GOgenes = resGO$FinalGOTermGenes ,
cutoff = cutoff, percent = percent, stp = stp )
newList <- c(newList, setNames(list(resSL), "semiLabeling" ))
################################################################################ semiSupervised
message("starting semi-supervised step...")
resSup <- semiSupervised(specExp = resClus$Y, geneLab = resSL$geneLabel,
model = model, kn = kn)
newList <- c(newList, setNames(list(resSup), "semiSupervised"))
################################################################################ geneOntology
geneLabel <- resSup$FinalLabeling
message("starting final gene ontology enrichment step...")
resFinal <- geneOntology(geneUniv = geneLabel$geneID,
clusLab = geneLabel$FinalLabel,
annotation_db = annotation_db,
direction = dir, ontology = onto, cond = condTest)
newList <- c(newList, setNames(list(resFinal), "final.GO"))
initial <- data.frame(geneID = resClus$geneID,
initialClusters = resClus$clusterLabels)
final <- data.frame(geneID = geneID,
finalClusters = resSup$FinalLabeling$FinalLabel)
clusterLabels <- inner_join(initial, final, by= "geneID")
newList <- c(setNames(list(clusterLabels), "clusterLabels"), newList)
remain <- setdiff(unique(clusterLabels$initialClusters),
unique(clusterLabels$finalClusters))
if(length(remain)== 1){
tt <- paste0("cluster ", remain)
temp <- paste0(tt, " is wiped out")
message(temp)
}else if(length(remain)){
tt <- paste0("clustes ", remain)
temp <- paste0(tt, " are wiped out")
message(temp)}
} # end of semiLabel
message("ezSGCP done!..\n")
newList <- c(setNames(list(semilabel), "semilabel"), newList)
return(newList)
}
