Nothing
setClass("BiclustSet",
representation(GenesMembership="matrix",ColumnMembership="matrix",
Number="numeric")
)
#constructor for the class BiclustSet
BiclustSet <-function(x,fabia.thresZ=0.5,fabia.thresL=NULL){myBiclustSet = new("BiclustSet",GenesMembership=x@RowxNumber, ColumnMembership=x@NumberxCol,
Number=x@Number)}
setGeneric("BiclustSet")
setMethod("BiclustSet",signature(x="Biclust"),
function(x){myBiclustSet = new("BiclustSet",GenesMembership=x@RowxNumber, ColumnMembership=x@NumberxCol,
Number=x@Number)})
setMethod("BiclustSet",signature("Factorization"),function(x,fabia.thresZ=0.5,fabia.thresL=NULL){
#require(fabia)
N <- x@p1
tmp <- extractBic(x,thresZ=fabia.thresZ,thresL=fabia.thresL)
X <- x@X
FabiaBicl <- tmp$numn
DataFabiaColB <- c()
DataFabiaRowB <- c()
for (j in 1:N){
colMem <- vector(length= ncol(X), mode="logical")
rowMem <- vector (length = nrow(X), mode = "logical")
if(length(unlist(FabiaBicl[j,2])) > 0){
for (i in unlist(FabiaBicl[j,2])) {colMem[i] <- TRUE}
for (i in unlist(FabiaBicl[j,1])) {rowMem[i] <- TRUE}
DataFabiaColB <- rbind(DataFabiaColB, colMem)
DataFabiaRowB <- cbind(DataFabiaRowB, rowMem)
}else next
}
myBiclustSet = new("BiclustSet",GenesMembership=DataFabiaRowB , ColumnMembership=DataFabiaColB,
Number=N)
} )
setMethod("BiclustSet",signature("list"),
function(x){
biclust1Number<- ncol(x$rows)
bicArows <- matrix(as.logical(x$rows),ncol=biclust1Number,byrow=T)
bicAcols <- matrix(as.logical(x$columns),nrow=biclust1Number)
myBiclustSet = new("BiclustSet",GenesMembership=bicArows, ColumnMembership=bicAcols,
Number=biclust1Number)
})
###**show and summary the same as for Biclust class******************************
setMethod("show", "BiclustSet",
function(object)
{
cat("\nAn object of class",class(object),"\n\n")
n<-object@Number
n<-min(c(n,5))
if(n>1)
{
cat("\nNumber of Clusters found: ",object@Number, "\n")
cat("\nFirst ",n," Cluster sizes:\n")
rowcolsizes<-rbind(colSums(object@GenesMembership[,1:n]),rowSums(object@ColumnMembership[1:n,]))
rownames(rowcolsizes)<-c("Number of Rows:","Number of Columns:")
colnames(rowcolsizes)<-paste("BC", 1:n)
#print.default(format(rowcolsizes, print.gap = 2, quote = FALSE))
print(rowcolsizes)
}
else
{
if(n==1) cat("\nThere was one cluster found with\n ",sum(object@GenesMembership[,1]), "Rows and ", sum(object@ColumnMembership), "columns")
if(n==0) cat("\nThere was no cluster found")
}
cat("\n\n")
})
setGeneric("summary")
setMethod("summary", "BiclustSet",
function(object)
{
cat("\nAn object of class",class(object),"\n\n")
n<-object@Number
if(n>1)
{
cat("\nNumber of Clusters found: ",object@Number, "\n")
cat("\nCluster sizes:\n")
rowcolsizes<-rbind(colSums(object@GenesMembership[,1:n]),rowSums(object@ColumnMembership[1:n,]))
rownames(rowcolsizes)<-c("Number of Rows:","Number of Columns:")
colnames(rowcolsizes)<-paste("BC", 1:n)
#print.default(format(rowcolsizes, print.gap = 2, quote = FALSE))
print(rowcolsizes)
}
else
{
if(n==1) cat("\nThere was one cluster found with\n ",sum(object@GenesMembership[,1]), "Rows and ", sum(object@ColumnMembership), "columns")
if(n==0) cat("\nThere was no cluster found")
}
cat("\n\n")
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.