On Mon, Mar 30, 2009 at 6:01 AM, Irene Gallego Romero <ig247@cam.ac.uk>wrote:

> Dear all,
>
> I have some very big data files that look something like this:
>
> id chr pos ihh1 ihh2 xpehh
> rs5748748 22 15795572 0.0230222 0.0268394 -0.153413
> rs5748755 22 15806401 0.0186084 0.0268672 -0.367296
> rs2385785 22 15807037 0.0198204 0.0186616 0.0602451
> rs1981707 22 15809384 0.0299685 0.0176768 0.527892
> rs1981708 22 15809434 0.0305465 0.0187227 0.489512
> rs11914222 22 15810040 0.0307183 0.0172399 0.577633
> rs4819923 22 15813210 0.02707 0.0159736 0.527491
> rs5994105 22 15813888 0.025202 0.0141296 0.578651
> rs5748760 22 15814084 0.0242894 0.0146486 0.505691
> rs2385786 22 15816846 0.0173057 0.0107816 0.473199
> rs1990483 22 15817310 0.0176641 0.0130525 0.302555
> rs5994110 22 15821524 0.0178411 0.0129001 0.324267
> rs17733785 22 15822154 0.0201797 0.0182093 0.102746
> rs7287116 22 15823131 0.0201993 0.0179028 0.12069
> rs5748765 22 15825502 0.0193195 0.0176513 0.090302
>
> I'm trying to extract the maximum and minimum xpehh (last column) values
> within a sliding window (non overlapping), of width 10000 (calculated
> relative to pos (third column)). However, as you can tell from the brief
> excerpt here, although all possible intervals will probably be covered by at
> least one data point, the number of data points will be variable
> (incidentally, if anyone knows of a way to obtain this number, that would be
> lovely), as will the spacing between them. Furthermore, values of chr
> (second column) will range from 1 to 22, and values of pos will be
> overlapping across them; I want to evaluate the window separately for each
> value of chr.
>

The IRanges package from the Bioconductor project attempts to solve problems
like these. For example, to count the number of overlapping intervals at a
given position in the chromosome, you would use the coverage() function. The
RangedData class is designed to store data like yours and rdapply() makes it
easy to perform operations one chromosome at a time.

That said, I don't think it has any easy way to solve your problem of
calculating quantiles. That's a feature that needs to be added to the
package. I could imagine something like (with the development version),
calling disjointBins() to separate the ranges in bins where there is no
overlap, then converting each bin into an Rle, and then using pmin/max on
the Rle objects in series to get your answer.

Anyway, you probably want to check out IRanges.

Michael


>
> I've looked at the help and FAQ on sliding windows, but I'm a relative
> newcomer to R and cannot find a way to do what I need to do. Everything I've
> managed to unearth so far seems geared towards smoother time series. Any
> help on this problem would be vastly appreciated.
>
> Thanks,
> Irene
>
> --
> Irene Gallego Romero
> Leverhulme Centre for Human Evolutionary Studies
> University of Cambridge
> Fitzwilliam St
> Cambridge
> CB2 1QH
> UK
>
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