[BioC] matrix transformation

[Bucher Elmar]

Dear Mailing List,

I wrote the following function "matrix2tuple.sf" to translate a "cartesian xy matrix" as a "tuple matrix", to store it in relational database. 
The code works fine for a test set. My problem is, my real matrix is 7000 x 10000 big, which ends up in 70'000'0000' tuples. 
Transformation takes days X(... 
Has anyone an idea, how I can optimize the described functions for speed? 

Best Wishes, Elmar Bucher



##### BEGIN CODE LISTING ####

matrix2tuple.sf <- function(xy.matrix.m = NULL) {
    tuple.m <- NULL 
    #x.length.v <- dim(xy.matrix.m)[2]
    #y.length.v <- dim(xy.matrix.m)[1]
    #for (x.v in (1:x.length.v)) {
    #for (y.v in (1:y.length.v)) {
    x.axis.v <- colnames(xy.matrix.m)
    y.axis.v <- rownames(xy.matrix.m)
    for (x.v in x.axis.v) {
        for (y.v in y.axis.v) {
            #cat(x.v, y.v, xy.matrix.m[y.v,x.v],"\n")
            tuple.v <- c(x.v, y.v, xy.matrix.m[y.v,x.v])
            if (is.null(tuple.v)) {
                tuple.m <- tuple.v 
            } else {
                tuple.m <- rbind(tuple.m, tuple.v)
            }            
        }
    }
    return(tuple.m)
}


put.db.sf <- function(conn.s4=NULL, x.v=NULL, y.v=NULL,  xy.v=NULL) {
    query.v <- paste("INSERT INTO matrixdbtb ('xaxis','yaxis','xy') VALUES('",x.v,"','",y.v,"','",xy.v,"');", sep ="")
    #catch.df <- dbGetQuery(conn.s4, query.v)
    cat(query.v, "\n")
}

## main ## 
matrix.m <- c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16")
dim(matrix.m) <- c(4,4) 
colnames(matrix.m) <- c("A","B","C","D")
rownames(matrix.m) <- c("a","b","c","d")
tuple.m <- matrix2tuple.sf (matrix.m)
for (i in 1: dim(tuple.m)[1]) { 
    put.db.sf(x.v=tuple.m[i,1],y.v=tuple.m[i,2],xy.v=tuple.m[i,3])
}                    

#### END CODE LISTING ########