To clarify, samplingRL is a RangesList, not samplingRL[[1]]. ---- Original message ---- >Date: Mon, 14 Feb 2011 10:00:15 +1100 (EST) >From: [email protected] (on behalf of Dario Strbenac ><[email protected]>) >Subject: [Bioc-sig-seq] viewApplying Efficiently >To: [email protected] > >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. > >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
-------------------------------------- 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
