Thanks for the intrusion! I have
options(stringsAsFactors=FALSE)
and Paul probably doesn't, so he saw factors where I saw characters.
Paul,
I saw your other note ... try this code
L <- nrow(df)
# assign a new bin every time chrom changes
prev.chrom <- c(NA, df$chrom[-L])
bin1 <- cumsum(is.na(prev.chrom) | df$chrom !=
levels(df$chrom)[prev.chrom])
# substract the minimum chromStart from each bin
min.start <- tapply(df$chromStart, bin1, min, na.rm=TRUE)[bin1]
# split bins further if chromStart >= 115341 + min.start
bin2 <- floor((df$chromStart - min.start) / 115341)
# combine the two bins into one
df$bin <- interaction(bin1, bin2)
df
Jean
Rui Barradas <ruipbarra...@sapo.pt> wrote on 07/02/2012 02:24:43 PM:
> Hello,
>
> Sorry to intrude, but I think it's a factor issue.
> Try the changing the disjunction to, (in multiline edit)
>
>
> new.bin <- is.na(prev.chrom) |
> df$chrom != levels(df$chrom)[prev.chrom] |
> delta.start >= 115341
>
> It should work, now.
>
> Hope this helps,
>
> Rui Barradas
>
> Em 02-07-2012 20:03, pguilha escreveu:
> > Jean,
> > It's crazy, I'm still getting 1,2,3,4,5,6 in the bin column.....
> > Also (this is an unrelated problem i think), unless I've misunderstood
> > it, I think your code will only create a new bin if the difference
> > between chromStart at i and i-1 position is >=115341....What I want is
> > for a new bin to be created each time the difference between
> > chromStart at i and i-j is >=115341, where 'i-j' corresponds to the
> > first row of the last bin....Im not sure if I'm being
> > clear...chromStart values correspond to coordinates along a chromosome
> > so I want to basically cut up each chromosome into sections/bins of
> > approximately 115341...
> >
> > thanks again for all your efforts with this, they're much appreciated!
> > Paul
> >
> > On 2 July 2012 19:36, Jean V Adams [via R]
> > <ml-node+s789695n4635185...@n4.nabble.com> wrote:
> >> Paul,
> >>
> >> Try this (I changed some of the object names, but the meat of the
code is
> >> the same):
> >>
> >> df <- 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)
> >> )
> >>
> >> # assign a new bin every time chrom changes and every time chromStart
> >> changes by 115341 or more
> >> L <- nrow(df)
> >> prev.chrom <- c(NA, df$chrom[-L])
> >> delta.start <- c(NA, df$chromStart[-1] - df$chromStart[-L])
> >> new.bin <- is.na(prev.chrom) | df$chrom != prev.chrom | delta.start
>=
> >> 115341
> >> df$bin <- cumsum(new.bin)
> >> df
> >>
> >>
> >> pguilha <[hidden email]> wrote on 07/02/2012 10:23:36 AM:
> >>
> >>> 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]
> >>> <[hidden email]> 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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