On 02/16/2011 06:13 AM, Michael Lawrence wrote: > On Tue, Feb 15, 2011 at 5:01 PM, supat thongjuea > <[email protected]>wrote: > >> Hi, >> >> I have two Rle views call chip.views and contr.views. I would like to speed >> up the iteration for getting the coefficient values from the linear >> regression model. >> I used sapply for those two Views but it is quite slow to get coefficient >> value from around 10,000 Views. Do you have any suggestion how to speed up >> this?. >> >> chip.cov <-coverage(chip.GRanges.uniq) >> contr.cov<-coverage(contr.GRanges.uniq) >> window.size=100000 >> step.size = window.size >> ends <- seq(from=window.size,to=chr.size,by=step.size) >> starts <- >> seq(from=1,to=chr.size-window.size,by=step.size) >> chip.views<-Views(chip.cov[[1]],starts,ends) >> contr.views<-Views(contr.cov[[1]],starts,ends) >> >> factor<-sapply(1:length(chip.views),function(x) >> >> lsfit(as.integer(chip.views[[x]]),as.integer(contr.views[[x]]))$coefficients[[2]]) >> >> > Not sure about speeding this up, but for the sake of clarity anyway, you > might want to use the viewApply() function instead of sapply here.
Supat -- you might try to profile your code to identify where the slowness is; see ?Rprof. If it is actually in lsfit then perhaps a little direct algebra on the two vectors (instead of lsfit) will more efficiently calculate the coefficient you're interested in. Martin > > Michael > > Best regards, >> Supat Thongjuea >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
