Thank you both very much! the factor issue was indeed solved by your
modifications, and Jean that last bit of code does exactly what I
need. Perfect!
thanks again
paul
On 2 July 2012 21:34, Jean V Adams [via R]
wrote:
> Thanks for the intrusion! I have
> options(stringsAsFactors=FALSE)
>
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$chrom[-L])
bin1 <- cumsum
Hello,
Sorry to intrude, but I think it's a factor issue.
Try the changing the disjunction to, (in multiline edit)
new.bin <- is.na(prev.chrom) |
df$chrom != levels(df$chrom)[prev.chrom] |
delta.start >= 115341
It should work, now.
Hope this helps,
Rui Barrada
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 >=115341What I want is
for a new bin to be
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, 2
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]
wrote:
> Paul,
>
> Are you submitting the exact code that I included in my previous e-mail?
> When I
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 1008910309 ZBTB33 10089 1
2 chr1 1013210536 TAF7_(SQ-8) 20221 1
3 chr2 10133
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 1008910309
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
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
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