Hi, if I have a DNAStringSet object, say 5 sequences, and I want to do a sliding window across those sequences and calculate `consensusMatrix` on only a some sites of the entire sequence, what is the best way to go about this? I think that for the selection of the sites I can use a mask, and I think I can also use a row mask to mask which sequences are not included, but how about the sliding windows? Do I have to use Ranges? and if so I or G ranges? Or do I have to use Views? I want to code a trial solution to this but I'm unsure which approach is the correct one to start with.

Thanks,

Ben.

Hi Ben,

If you want to calculate consensusMatrix on only some sites of the entire sequences, why do you need a sliding window? Also please clarify what would be the input of consensusMatrix() at each site? Would it be 5 subsequences, one per sequence in the original DNAStringSet object? Would these subsequences be taken from the same window (e.g. position 50-70) on each original sequence? That suggests that the original sequences have the same length. Is that the case?

So for example to calculate consensusMatrix for a window of width 20 at positions 50, 75, 90, 108:

library(Biostrings)
file <- system.file("extdata", "someORF.fa", package="Biostrings")
orf <- readDNAStringSet(file)  # DNAStringSet object with 7 sequences
my_pos <- c(50, 75, 90, 108)
lapply(my_pos, function(pos) consensusMatrix(subseq(orf, pos, width=20)))

This returns a list of consensus matrices, one per position.

This won't be efficient if you have tens of thousands of positions. But before we worry about performance, let's make sure we understand what you are trying to do exactly. Showing us some naive code might help.

Cheers,

H.