Your description was too general for me to know exactly what you want but
perhaps this will help you solve your own problem
set.seed(123)
evtlist = sample(c('fwd','rev'),100,replace=TRUE)
evtlist
[1] "fwd" "rev" "fwd" "rev" "rev" "fwd" "rev" "rev" "rev" "fwd" "rev"
"fwd" "rev"
[14] "rev" "fwd" "rev" "fwd" "fwd" "fwd" "rev" "rev" "rev" "rev" "rev" "rev"
"rev"
[27] "rev" "rev" "fwd" "fwd" "rev" "rev" "rev" "rev" "fwd" "fwd" "rev" "fwd"
"fwd"
[40] "fwd" "fwd" "fwd" "fwd" "fwd" "fwd" "fwd" "fwd" "fwd" "fwd" "rev" "fwd"
"fwd"
[53] "rev" "fwd" "rev" "fwd" "fwd" "rev" "rev" "fwd" "rev" "fwd" "fwd" "fwd"
"rev"
[66] "fwd" "rev" "rev" "rev" "fwd" "rev" "rev" "rev" "fwd" "fwd" "fwd" "fwd"
"rev"
[79] "fwd" "fwd" "fwd" "rev" "fwd" "rev" "fwd" "fwd" "rev" "rev" "rev" "fwd"
"fwd"
[92] "rev" "fwd" "rev" "fwd" "fwd" "rev" "fwd" "fwd" "rev"
rle(evtlist)
Run Length Encoding
lengths: int [1:50] 1 1 1 2 1 3 1 1 1 2 ...
values : chr [1:50] "fwd" "rev" "fwd" "rev" "fwd" "rev" "fwd" "rev" "fwd"
...
rle(evtlist)$lengths
[1] 1 1 1 2 1 3 1 1 1 2 1 1 3 9 2 4 2 1 12 1 2 1 1 1
2 2 1 1
[29] 3 1 1 3 1 3 4 1 3 1 1 1 2 3 2 1 1 1 2 1 2 1
see ?rle
Rob
-----Original Message-----
From: Mark Hills
Sent: Friday, March 16, 2012 3:55 PM
To: r-help@r-project.org
Subject: [R] Identifying a change in events between bins
Hi there,
First off, despite this being my first post here, I have scanned the R help
forums a lot in the past few months to help with some questions, so a big
thank you to the community as a whole for being so helpful!
I'm somewhat of an R newbie, and have run up against a problem that I can't
seem to solve. If anyone is able to help I would really appreciate it!
I'm looking at a number of events across a chromosome, and have written a
program that collects them into different bins, based on a specified
binsize. The events are directional, either forward or reverse, and a
chromosome can either be fwd/fwd (all the events fall into the fwd bins),
rev/rev (all the events fall into the rev bins) or fwd/rev (events are
evenly split). In some cases, chromosomes switch from one state to another
(eg fwd/fwd to fwd/rev). There are a number of rules that dictate my data.
First, while there is stochastic variation, the sum of fwd and rev in each
bin should have approximately the same value. If I were to take the total
number of events and divide them by the number of bins to get an average
count per bin, I would expect approximately that value in each bin; in the
case of fwd/fwd it would be about average number in the fwd column and close
to zero in the rev column, in rev/rev it would be about the average number
in the rev column and close to zero in the fwd column, and in fwd/rev it
would be about half the average number in both.
Hopefully my png attachment worked and you can see an example. The top plot
shows fwd reads, the 2nd shows rev reads and the third shows fwd minus rev
reads.
What I would like to be able to do is to automatically assign regions in
which the chromosome switches from one state to another. From the graphs
(and from the read.table output below) you can see that this particular
chromosome is fwd/fwd from bin 1 to 59, fwd/rev from bin 61 to 73, and
rev/rev for the remainder of the chromosomes.
These are generated from a read.table that looks like this:
bin fwd rev
50 484 2
51 366 4
52 527 6
53 635 2
54 573 6
55 506 4
56 600 6
57 560 2
58 504 2
59 545 0
60 501 68
61 419 223
62 252 109
63 259 138
64 355 189
65 218 125
66 140 57
67 45 31
68 276 144
69 263 152
70 330 193
71 439 204
72 347 207
73 10 611
74 6 619
75 2 578
76 7 372
77 6 436
78 4 373
79 8 417
80 2 276
My question is this:
1. Is there an obvious way to automatically identify these regions?
I am not sure how I can go about scanning previous lines within a read.table
to find a point at which the values change. In the above example, I would
like the program to identify that the fwd graph shifts from ~1x the average
to ~0.5x the average between bin 61 and 62, and from ~0.5x the average to
~0x the average between bin 72 and 73. Conversely I'd like to identify the
rev graph shifting from ~0x average to ~0.5x average between bins 59 and 60,
and from 0.5x average to 1x average from bin 72 to 73. Finally, I'd like to
cross-reference the output from fwd and rev to only pull out reciprocal
switches (ie those that occur within 3 bins of each other in both fwd and
rev data sets).
What I've been trying to gt to work is to generate values based on 0, 0.5
and 1x the average events, and trying to pull out the range of bins that
fall into each of those categories (possibly 1 SD higher or lower to account
for the stochastic variation), but I'm not really sure how to go about that.
2. If I can find a way to identify a shift between bins, is there any way to
then look in smaller bin sizes across those regions. The bins shown above
are for 200,000 bases of DNA. If my program automatically found an event
between bin 72 and 73 (14,400,000 bases to 14,600,000), is it possible to
feed that region into say 50,000 base bins to narrow down the location of
the event?
I'm not sure if either of these questions is a simple task or incredibly
time consuming and inappropriate to ask a message board. If you can offer
any advice though, I would really appreciate it!
Thanks,
Mark
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
------------------------------------------
Robert W. Baer, Ph.D.
Professor of Physiology
Kirksville College of Osteopathic Medicine
A. T. Still University of Health Sciences
800 W. Jefferson St.
Kirksville, MO 63501
660-626-2322
FAX 660-626-2965
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
