[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Tue Sep 6 17:04:46 CEST 2011
Sonia,
Problem 1 occurs when * was allowed as strand values. It has been fixed in
the released version 1.9.0.
Please let us know if you still have problems. Many thanks for your
feedback!
Best regards,
Julie
On 9/1/11 10:06 PM, "Julie Zhu" <julie.zhu at umassmed.edu> wrote:
> Sonia,
>
> The bug (problem 2) was introduced with the addition of parameter select for
> replacing parameter multiple in the dev version. Now the bug is fixed in
> ChIPpeakAnno_2.0.4. Please let us know if the problem persists.
>
> Many thanks for your feedback!
>
> Best regards,
>
> Julie
>
> On 9/1/11 4:02 PM, "Ou, Jianhong" <Jianhong.Ou at umassmed.edu> wrote:
>
>> 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 8/31/11 3:52 PM, "Sonia Leach" <sonia.leach at gmail.com> wrote:
>
>> 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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>
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