[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2

Thu Sep 1 22:02:55 CEST 2011

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.ou at 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.Ou at 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.ou at umassmed.edu
>> 
>> 
>> On Aug 31, 2011, at 4:17 PM, Zhu, Lihua (Julie) wrote:
>> 
>>> 
>>> ------ Forwarded Message
>>> From: Sonia Leach <sonia.leach at gmail.com>
>>> Date: Wed, 31 Aug 2011 15:52:43 -0400
>>> To: "bioc-sig-sequencing at r-project.org" <bioc-sig-sequencing at 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
>>>> 
>>> 
>>> _______________________________________________
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>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>> 
>>> ------ End of Forwarded Message
>>> 
>> 
>> 
>> 