On Thu, Nov 25, 2010 at 12:10 AM, Ulrike Goebel
<ugoebel@mpiz-koeln.mpg.de>wrote:

> Hello,
>
> "precede" and "follow" seems to do just  the opposite of  what is described
>  in the help page:
>
> > test <- IRanges(start=c(1,6,20), end=c(5,22,40))
> > precede(test)
> [1]  2 NA NA
> These are the ranges that *follow* the query ranges ..
>
> > follow(test)
> [1] NA  1  1
> .. and these are the preceding ranges ...
>
> Is this meant to be like this ?
>
>
Yes, it's the docs that are wrong. precede() could be called "find the
interval that each query precedes". It has the same semantic as
findOverlaps, previously called overlap(), which asks "find the interval(s)
that each query overlaps".

I've tweaked the docs in devel.

Thanks,
Michael



> Best, Ulrike
>
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] Ringo_1.12.0       Matrix_0.999375-38 lattice_0.18-5     limma_3.4.3
> [5] RColorBrewer_1.0-2 affy_1.26.1        Biobase_2.8.0      plotrix_2.9-5
> [9] IRanges_1.6.11
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         annotate_1.26.1       AnnotationDbi_1.10.2
> [4] DBI_0.2-5             genefilter_1.30.0     preprocessCore_1.10.0
> [7] RSQLite_0.9-2         splines_2.11.0        survival_2.35-8
> [10] tools_2.11.0          xtable_1.5-6
>
>
> --
>  Dr. Ulrike Goebel
>  Max-Planck Institute for Plant Breeding Research
>  Carl-von-Linne Weg 10
>  50829 Cologne
>  Germany
>  +49(0) 221 5062 448            **** NOTE NEW PHONE NUMBER !!! ****
>
> _______________________________________________
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>

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