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