Hi Sonia, Thank you very much for your bug reports.
I checked about the ChIPpeakAnno_1.8.0, I found that the binary file is different from source code. If possible, could you install from the source instead? This problem 1 is fixed in the source. And we will rebuilt the binary soon. And we will fix the 2nd issue soon. Thank you again. Yours sincerely, Jianhong Ou jianhong...@umassmed.edu On Sep 1, 2011, at 11:12 AM, Sonia Leach wrote: > Oh, I thought I mentioned it was just a straight table dump from UCSC > goldenpath, but to be more specific: > > 1. go to http://genome.ucsc.edu/cgi-bin/hgGateway > 2. Click the 'Tables' tab > 3. Make sure you use genome:Human, assembly:Feb 2009, group:Genes and > Gene Prediction Tracks, track:UCSC Genes, table: knownGene > 4. For output format: BED - browser extensible data, fill in output > file with "UCSC_knownGene.hg19.bed" > 5. Click 'get output' and choose 'Create one BED record per 'Whole > Gene'' and then hit getBed. > > Thanks for looking into this. > Sonia > > On Thu, Sep 1, 2011 at 7:08 AM, Ou, Jianhong <jianhong...@umassmed.edu> wrote: >> Hi Sonia, >> >> Could you tell me the details about how to generate the annotation file >> Annots/UCSC_knownGene.hg19.bed? >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong...@umassmed.edu >> >> >> On Aug 31, 2011, at 4:17 PM, Zhu, Lihua (Julie) wrote: >> >>> >>> ------ Forwarded Message >>> From: Sonia Leach <sonia.le...@gmail.com> >>> Date: Wed, 31 Aug 2011 15:52:43 -0400 >>> To: "bioc-sig-sequencing@r-project.org" <bioc-sig-sequencing@r-project.org> >>> Subject: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in >>> R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 >>> >>> I had a problem with the original ChIPpeakAnno distribution >>> ChIPpeakAnno_1.8.0 for R2.13 where depending on the number of spaces >>> in the RangedData Annotation object sent to annotatePeakInBatch, I >>> would get the error: >>> Error in FUN(1L[[1L]], ...) : object 'r' not found >>> (see Problem 1 below) which went away when I downloaded the >>> development version R2.13/ChIPpeakAnno_2.0.2 >>> >>> However, then I had the problem that calling annotatePeakInBatch(..., >>> output="overlapping", multiple=FALSE) returned the same number of >>> answers as annotatePeakInBatch(..., output="overlapping", >>> multiple=TRUE) (see Problem 2 below). Obviously, the work around is to >>> take one hit from among the multiples returned but this should be >>> fixed. >>> >>> The annotation file I used is just a bed6 dump from UCSC goldenpath. >>> >>> ============ problem 1: >>> library(ChIPpeakAnno) >>> >>> myPeak = RangedData(IRanges(start = c(17208381), end = c(17208381), names = >>> c("S >>> ite1")),space = c("chr1"),strand = c('+')) >>> >>> ## This object has 25 spaces for chr1..22,X,Y,M >>> UCSC = read.delim('Annots/UCSC_knownGene.hg19.bed',header=FALSE) >>> UCSC_rangeD = RangedData(IRanges(start= UCSC[,2], end= UCSC[,3], >>> names=UCSC[,4]) >>> , space=as.character(UCSC[,1]),strand=UCSC[,6]) >>> >>> ## This object has just 1 space but the same data as UCSC_rangedD[868,] >>> feature = RangedData(IRanges(start = c(17066767), end = c(17267729), names = >>> c(" >>> Site1")),space = c("chr1"),strand = c('+')) >>> >>> ## with UCSC_rangeD[868,], gives error in R2.13/ChIPpeakAnno_1.8.0 >>> ## Error in FUN(1L[[1L]], ...) : object 'r' not found >>> annotation = annotatePeakInBatch(myPeak, AnnotationData=UCSC_rangeD[868,], >>> outpu >>> t="overlapping", maxgap=0, multiple=FALSE) >>> >>> ## with 1-space feature, no error >>> annotation = annotatePeakInBatch(myPeak, AnnotationData=feature, >>> output="overlap >>> ping", maxgap=0, multiple=FALSE) >>> >>> <sorry, I no longer have the session info for this run - but it is the >>> basic R2.13 install plus biocLite(ChIPpeakAnno), and should have the >>> same versions as the session info shown for problem 2 below, minus the >>> new dev version for ChIPpeakAnno (i.e. everything the same as below, >>> except ChIPpeakAnno_2.0.2.tar.gz, gplots_2.8.0.tar.gz, >>> caTools_1.12.tar.gz, gdata_2.8.2.tar.gz, gtools_2.6.2.tar.gz) >>>> >>> >>> ======== Problem 2 >>> R version 2.13.0 (2011-04-13) >>> Copyright (C) 2011 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>>> library(ChIPpeakAnno) >>> Warning message: >>> replacing previous import 'space' when loading 'IRanges' >>>> UCSC = read.delim('Annots/UCSC_knownGene.hg19.bed',header=FALSE) >>>> UCSC_rangeD = RangedData(IRanges(start= UCSC[,2], end= UCSC[,3], >>> names=UCSC[,4]), space=as.character(UCSC[,1]),strand=UCSC[,6]) >>>> data = unique(read.table(file[i], sep="\t", header=FALSE)) >>>> ids = sub("ID=(\\d+);.+", "ID\\1", data[,9], perl=TRUE) >>>> data_rangeD = RangedData(IRanges(start=data$V4, end=data$V5, >>> names=paste(ids,data$V3, sep="_")), space=data$V1, strand="+") >>>> dim(data_rangeD) >>> [1] 19501 1 >>>> annotationU = annotatePeakInBatch(data_rangeD, AnnotationData=UCSC_rangeD, >>>> out >>> put="overlapping", maxgap=0, multiple=FALSE) >>>> dim(annotationU) >>> [1] 16777 9 >>>> annotationU = annotatePeakInBatch(data_rangeD, AnnotationData=UCSC_rangeD, >>>> out >>> put="overlapping", maxgap=0, multiple=TRUE) >>>> dim(annotationU) >>> [1] 16777 9 >>>> sessionInfo() >>> R version 2.13.0 (2011-04-13) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> 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 >>> [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] ChIPpeakAnno_2.0.2 gplots_2.8.0 >>> [3] caTools_1.12 bitops_1.0-4.1 >>> [5] gdata_2.8.2 gtools_2.6.2 >>> [7] limma_3.8.3 org.Hs.eg.db_2.5.0 >>> [9] GO.db_2.5.0 RSQLite_0.9-4 >>> [11] DBI_0.2-5 AnnotationDbi_1.14.1 >>> [13] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.20.0 >>> [15] GenomicRanges_1.4.8 Biostrings_2.20.2 >>> [17] IRanges_1.10.6 multtest_2.8.0 >>> [19] Biobase_2.12.2 biomaRt_2.8.1 >>> >>> loaded via a namespace (and not attached): >>> [1] MASS_7.3-12 RCurl_1.6-9 splines_2.13.0 survival_2.36-5 >>> [5] XML_3.4-2 >>>> >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> Bioc-sig-sequencing@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >>> ------ End of Forwarded Message >>> >> >> >> _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
