Hi ; I would appreciate a piece of advice on the following ;

I would like to append a GRange object "interactions" that is initially EMPTY ;

interactions <- append(interactions, interactions_chr[k])

how do I initialize a GRange object "initeractions" that is EMPTY at the very beginning ?

thanks ,

bogdan

Hi Bodgan,

You create an empty GRanges object by calling GRanges().

Note that growing an object in a loop with something like

interactions <- GRanges()
for (i in seq_len(N)) {
    gr <- ... make some GRanges object ...    
    interactions <- append(interactions, gr)
}

is generally very inefficient and should be avoided.

If you know in advance how many iterations you're going to do, it is a lot more efficient to do:

interactions <- vector(mode="list", length=N)
for (i in seq_len(N)) {
    gr <- ... make some GRanges object ...   
    interactions[[i]] <- gr
}
interactions <- do.call(c, interactions)

Alternatively, you can replace the for loop by a call to lapply() which is more elegant but does basically the same.

H.

Dear Herve,

many thanks for your reply: it is very helpful. happy weekend !

-- bogdan