On Thu, Nov 25, 2010 at 12:10 AM, Ulrike Goebel <[email protected]>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 !!! **** > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
