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. 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
