Jean, that's exactly what it should be, but yes I copied and pasted
from your email so I don't see how I could have introduced an error in
there....
paul
On 2 July 2012 15:57, Jean V Adams [via R]
<ml-node+s789695n4635144...@n4.nabble.com> wrote:
> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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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