Hi Dario, The strand was converted to level type automatically, I will fix it as soon as I get access to the computer with SVN installed. Meanwhile, please use the following code snippet, i.e., -1 as minus strand and 1 as positive strand. Thanks! Best regards, Julie peaksT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1000, 2000, 3000), end = c(2000, 3000, 4000)) featuresT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1500, 2500, 3500), end = c(2500, 3500, 4500), strand = c(-1)) peaks <- RangedData(space = peaksT$chr, ranges = IRanges(start = peaksT$start, end = peaksT$end)) features <- RangedData(space = featuresT$chr, strand = featuresT$strand, ranges = IRanges(start = featuresT$start, end = featuresT$end)) annotatePeakInBatch(peaks, AnnotationData = features) RangedData with 3 rows and 9 value columns across 1 space space ranges | peak strand feature start_position <character> <iranges> | <character> <character> <character> <numeric> 1 1 chr1 [1000, 2000] | 1 -1 1 1500 2 1 chr1 [2000, 3000] | 2 -1 1 1500 3 2 chr1 [3000, 4000] | 3 -1 2 2500 end_position insideFeature distancetoFeature shortestDistance fromOverlappingOrNearest <numeric> <character> <numeric> <numeric> <character> 1 1 2500 overlapEnd 1500 500 NearestStart 2 1 2500 overlapStart 500 500 NearestStart 3 2 3500 overlapStart 500 500 NearestStart On 5/16/10 6:59 PM, "Dario Strbenac" <d.strbenac@garvan.org.au> wrote: Hello, Here is my little test script : peaksT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1000, 2000, 3000), end = c(2000, 3000, 4000), strand = c('+', '+', '+')) featuresT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1500, 2500, 3500), end = c(2500, 3500, 4500), strand = c('-', '-', '-')) peaks <- RangedData(space = peaksT$chr, strand = peaksT$strand, ranges = IRanges(start = peaksT$start, end = peaksT$end)) features <- RangedData(space = featuresT$chr, strand = featuresT$strand, ranges = IRanges(start = featuresT$start, end = featuresT$end)) annotatePeakInBatch(peaks, AnnotationData = features)) The sessionInfo is : R version 2.11.0 (2010-04-22) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.4.0 limma_3.4.0 org.Hs.eg.db_2.4.1 GO.db_2.4.1 RSQLite_0.9-0 [6] DBI_0.2-5 AnnotationDbi_1.10.1 BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.0 GenomicRanges_1.0.1 [11] Biostrings_2.16.0 IRanges_1.6.0 multtest_2.4.0 Biobase_2.8.0 biomaRt_2.4.0 loaded via a namespace (and not attached): [1] MASS_7.3-5 RCurl_1.3-1 splines_2.11.0 survival_2.35-8 tools_2.11.0 XML_2.8-1 Thanks, Dario. ---- Original message ---- >Date: Fri, 14 May 2010 07:38:20 -0400 >From: "Zhu, Julie" <julie.zhu@umassmed.edu> >Subject: Re: [BioC] ChIPpeakAnno Critical Bug >To: "D.Strbenac@garvan.org.au" <d.strbenac@garvan.org.au>, "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> > > Hi Dario, > > Could you please send your code snippets and session > info? Thanks! > > Best regards, > > Julie > > On 5/14/10 1:48 AM, "Dario Strbenac" > <d.strbenac@garvan.org.au> wrote: > > Hello, > > It seems that the annotatePeakInBatch function > completely ignores strand information : > > > peaks > RangedData with 3 rows and 1 value column across 1 > space > space ranges | strand > <character> <iranges> | <factor> > 1 chr1 [1000, 2000] | + > 2 chr1 [2000, 3000] | + > 3 chr1 [3000, 4000] | + > > features > RangedData with 3 rows and 1 value column across 1 > space > space ranges | strand > <character> <iranges> | <factor> > 1 chr1 [1500, 2500] | - > 2 chr1 [2500, 3500] | - > 3 chr1 [3500, 4500] | - > > annotatePeakInBatch(peaks, AnnotationData = > features) > RangedData with 3 rows and 9 value columns across > 1 space > space ranges | peak > strand feature start_position > end_position insideFeature distancetoFeature > shortestDistance fromOverlappingOrNearest > <character> <iranges> | <character> > <character> <character> <numeric> > <numeric> <character> <numeric> > <numeric> <character> > 1 1 chr1 [1000, 2000] | 1 > 1 1 1500 > 2500 overlapStart -500 > 500 NearestStart > 2 1 chr1 [2000, 3000] | 2 > 1 1 1500 > 2500 overlapEnd 500 > 500 NearestStart > 3 2 chr1 [3000, 4000] | 3 > 1 2 2500 > 3500 overlapEnd 500 > 500 NearestStart > > Shouldn't get anything overlapping ... > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]