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]])
Best regards,
Supat Thongjuea
[[alternative HTML version deleted]]
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
