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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