[BioC] matrix transformation

Bucher Elmar Ext-Elmar.Bucher at vtt.fi
Mon Oct 18 11:41:18 CEST 2010

```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 ########

```