Paul,
Are you submitting the exact code that I included in my previous e-mail?
When I submit that code, I get this ...
chrom chromStart chromEnd name cumsum bin
1 chr1 10089 10309 ZBTB33 10089 1
2 chr1 10132 10536 TAF7_(SQ-8) 20221 1
3 chr2 10133 10362 Pol2-4H8 30354 2
4 chr2 10148 10418 MafF_(M8194) 40502 2
5 chr2 210382 210578 ZBTB33 50884 3
6 chr2 216132 216352 CTCF 67016 3
Jean
Paul Guilhamon <paul.guilha...@gmail.com> wrote on 07/02/2012 08:59:00 AM:
> Thanks for your reply Jean,
>
> I think your interpretation is correct but when I run your code I end
> up with the below dataframe and obviously the bins created there don't
> correspond to a chromStart change of 115341:
>
> chrom chromStart chromEnd name cumsum bin
> 1 chr1 10089 10309 ZBTB33 10089 1
> 2 chr1 10132 10536 TAF7_(SQ-8) 20221 2
> 3 chr2 10133 10362 Pol2-4H8 30354 3
> 4 chr2 10148 10418 MafF_(M8194) 40502 4
> 5 chr2 210382 210578 ZBTB33 50884 5
> 6 chr2 216132 216352 CTCF 67016 6
>
> the first two rows should have the same bin number (same chrom,
> <115341 diff), then rows 3&4 should be in another bin (different chrom
> from rows 1&2, <115341 diff), and rows 5&6 in another one (same chrom
> but >115341 difference between row 4 and row 5).
>
> it seems the new.bin line of your code isn't quite doing what it
> should but I can't pinpoint the error there...
> Paul
>
>
> On 2 July 2012 14:19, Jean V Adams <jvad...@usgs.gov> wrote:
> > Paul,
> >
> > My interpretation is that you are trying to assign a new bin number to
a row
> > every time the variable chrom changes and every time the variable
chromStart
> > changes by 115341 or more. Is that right? If so, you don't need a
loop at
> > all. Check out the code below. I made a couple changes to the
all.tf7
> > example data frame so that it would have two changes in bin number,
one
> > based on the chrom variable and one based on the chromStart variable.
> >
> > Jean
> >
> > all.tf7 <- data.frame(
> > chrom = c("chr1", "chr1", "chr2", "chr2", "chr2", "chr2"),
> > chromStart = c(10089, 10132, 10133, 10148, 210382, 216132),
> > chromEnd = c(10309, 10536, 10362, 10418, 210578, 216352),
> > name = c("ZBTB33", "TAF7_(SQ-8)", "Pol2-4H8", "MafF_(M8194)",
> > "ZBTB33", "CTCF"),
> > cumsum = c(10089, 20221, 30354, 40502, 50884, 67016),
> > bin = rep(NA, 6)
> > )
> >
> > # assign a new bin every time chrom changes and every time chromStart
> > changes by 115341 or more
> > L <- nrow(all.tf7)
> > prev.chrom <- c(NA, all.tf7$chrom[-L])
> > delta.start <- c(NA, all.tf7$chromStart[-1] - all.tf7$chromStart[-L])
> > new.bin <- is.na(prev.chrom) | all.tf7$chrom != prev.chrom |
delta.start >=
> > 115341
> > all.tf7$bin <- cumsum(new.bin)
> > all.tf7
> >
> >
> > pguilha <paul.guilha...@gmail.com> wrote on 07/02/2012 06:25:13 AM:
> >
> >> Hello all,
> >>
> >> I have written a for loop to act on a dataframe with close to
3million
> >> rows
> >> and 6 columns and I would like to pass it to apply() to speed the
process
> >> up
> >> (I let the loop run for 2 days before stopping it and it had only
gone
> >> through 200,000 rows) but I am really struggling to find a way to
pass the
> >> arguments. Below are the loop and the head of the dataframe I am
working
> >> on.
> >> Any hints would be much appreciated, thank you! (I have searched for
this
> >> but could not find any other posts doing quite what I want)
> >> Paul
> >>
> >> x<-as.numeric(all.tf7[1,2])
> >> for (i in 2:nrow(all.tf7)) {
> >> if (all.tf7[i,1]==all.tf7[i-1,1] & (all.tf7[i,2]-x)<115341)
> >> all.tf7[i,6]<-all.tf7[i-1,6]
> >> else if (all.tf7[i,1]==all.tf7[i-1,1] & (all.tf7[i,2]-x)>=115341) {
> >> all.tf7[i,6]<-(all.tf7[i-1,6]+1)
> >> x<-as.numeric(all.tf7[i,2]) }
> >> else if (all.tf7[i,1]!=all.tf7[i-1,1]) {
> >> all.tf7[i,6]<-(all.tf7[i-1,6]+1)
> >> x<-as.numeric(all.tf7[i,2]) }
> >> }
> >>
> >> #the aim here is to attribute a bin number to each row so that I can
then
> >> split the dataframe according to those bins.
> >>
> >>
> >> chrom chromStart chromEnd name cumsum bin
> >> chr1 10089 10309 ZBTB33 10089 1
> >> chr1 10132 10536 TAF7_(SQ-8) 20221 1
> >> chr1 10133 10362 Pol2-4H8 30354 1
> >> chr1 10148 10418 MafF_(M8194) 40502 1
> >> chr1 10382 10578 ZBTB33 50884 1
> >> chr1 16132 16352 CTCF 67016 1
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