On 02/13/2011 03:00 PM, Dario Strbenac wrote: > Hello, > > I have an RleList of about 17000 Rles and I'd like to get the regularly spaced values out of each one of them and have a list of vectors of numbers as the result.
Maybe along the lines of elt <- Rle(as.numeric(floor(runif(50100, 1, 2.2)))) # simulated m <- Rle(rep(c(FALSE, TRUE), 100), rep(c(500, 1), 100)) # mask as.numeric((elt * m)[m]) ? This might be in an lapply on the RleList; m would have to be constructed to be the right length for each element. Martin > > e.g. my views locations is 17000 of these : > >> samplingRL[[1]] # is a RangesList > IRanges of length 101 > start end width > [1] 501 501 1 > [2] 1001 1001 1 > [3] 1501 1501 1 > [4] 2001 2001 1 > [5] 2501 2501 1 > [6] 3001 3001 1 > [7] 3501 3501 1 > [8] 4001 4001 1 > [9] 4501 4501 1 > ... ... ... ... > [93] 46501 46501 1 > [94] 47001 47001 1 > [95] 47501 47501 1 > [96] 48001 48001 1 > [97] 48501 48501 1 > [98] 49001 49001 1 > [99] 49501 49501 1 > [100] 50001 50001 1 > [101] 50501 50501 1 > > and my RleList has data like : > >> rleList[[1]] > 'numeric' Rle of length 51001 with 38620 runs > Lengths: 501 1 ... 1089 > Values : 0.671728853793319 0.677726432845045 ... 0.224909214439609 > > I do the following to get the sampling position values in one step, but it > uses up over 20 GB RAM in a matter of seconds, and I have to kill the process. > > result <- viewApply(Views(rleList, samplingRL), function(samples) > as.numeric(samples), simplify = TRUE) > > Is there a better way ? > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
