On 02/13/2011 04:44 PM, Martin Morgan wrote: > 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])
just i = seq(501, length(elt), by=500) as.numeric(elt[i]) > > ? 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
