[BioC] ChIPpeakAnno annotatePeakInBatch error message
Zhu, Julie
Julie.Zhu at umassmed.edu
Thu May 27 20:26:12 CEST 2010
Hi Dario,
Thanks for the vigorous test of the new feature!
The peak dataset contains chrX_random that is not in the feature dataset. I added is.na check on the strand which should fix the problem. I also attached the annotated Dataset. Please let me know if you encounter any problem.
Best regards,
Julie
On 5/26/10 11:00 PM, "Dario Strbenac" <D.Strbenac at garvan.org.au> wrote:
Hello,
Yes, I encountered the same problem again. This time I tried the code on my full table of data. This is my script. All the files it refers to are web accessible, so that you can replicate it too. I am definitely using version 1.5.3 of the package.
CpGIslandsTable <- read.table("http://129.94.136.7/file_dump/dario/hg18_CpG_Islands.bed", sep = '\t', stringsAsFactors = FALSE)
genesTable <- read.csv("http://129.94.136.7/file_dump/dario/humanGenomeAnnotation.csv", stringsAsFactors = FALSE)
colnames(CpGIslandsTable) <- c("chr", "start", "end", "name")
peaksRangedData <- RangedData(space = CpGIslandsTable$chr, ranges = IRanges(start = CpGIslandsTable$start, end = CpGIslandsTable$end))
featuresRangedData <- RangedData(name = genesTable$name, space = genesTable$chr, strand = genesTable$strand, ranges = IRanges(start = genesTable$start, end = genesTable$end))
featureLoc <- "TSS"
annotatePeakInBatch(peaksRangedData, AnnotationData = featuresRangedData, PeakLocForDistance = "middle")
> sessionInfo()
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_1.5.3 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 XML_2.8-1
---- Original message ----
>Date: Mon, 24 May 2010 22:57:47 -0400
>From: "Zhu, Julie" <Julie.Zhu at umassmed.edu>
>Subject: Re: [BioC] ChIPpeakAnno annotatePeakInBatch error message
>To: "D.Strbenac at garvan.org.au" <D.Strbenac at garvan.org.au>, "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>
> Hi Dario,
>
> Please download dev 1.5.3 version of ChIPpeakAnno
> and let me know if you encounter any problem.
> Thanks!
>
> Best regards,
>
> Julie
>
> annotatePeakInBatch(peaksRangedData, AnnotationData
> = featuresRangedData, PeakLocForDistance = "middle")
> RangedData with 6 rows and 9 value columns across 2
> spaces
> space ranges | peak
> strand feature start_position end_position
> insideFeature distancetoFeature
> <character> <IRanges> | <character>
> <character> <character> <numeric> <numeric>
> <character> <numeric>
> 1 1 chr1 [ 2000010, 2000310] | 1
> + 1 1e+06 2.0e+06
> downstream 1000160
> 2 2 chr1 [19000000, 19000300] | 2
> - 2 1e+07 2.0e+07
> inside 999850
> 3 2 chr1 [30000000, 30000300] | 3
> - 2 1e+07 2.0e+07
> upstream -10000150
> 4 4 chr2 [ 300, 600] | 4
> + 4 1e+03 5.0e+03
> upstream -550
> 6 6 chr2 [ 100000, 100300] | 6
> + 6 1e+04 1.5e+04
> downstream 90150
> 5 5 chr2 [ 5500, 5800] | 5
> - 5 6e+03 7.0e+03
> downstream 1350
> shortestDistance fromOverlappingOrNearest
> <numeric> <character>
> 1 1 10 NearestStart
> 2 2 999700 NearestStart
> 3 2 10000000 NearestStart
> 4 4 400 NearestStart
> 6 6 85000 NearestStart
> 5 5 200 NearestStart
>
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-apple-darwin9.8.0
>
> locale:
> [1]
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] ChIPpeakAnno_1.5.3 limma_3.4.0
> org.Hs.eg.db_2.4.1
>
> [4] GO.db_2.4.1
> RSQLite_0.9-0
> DBI_0.2-5
>
> [7] AnnotationDbi_1.10.1
> BSgenome.Ecoli.NCBI.20080805_1.3.16
> BSgenome_1.16.1
> [10] GenomicRanges_1.0.1
> Biostrings_2.16.0
> IRanges_1.6.1
>
> [13] multtest_2.4.0
> Biobase_2.8.0
> biomaRt_2.4.0
>
>
> On 5/24/10 5:10 AM, "Dario Strbenac"
> <D.Strbenac at garvan.org.au> wrote:
>
> Hello,
>
> I made another small example of using
> annoPeakInBatch to demonstrate to a friend, but it
> has crashed. It's similar to the other example but
> with different data. I'm not sure why it is
> happening.
>
> Here is my small example:
>
> peaksT <- data.frame(chr = c("chr1", "chr1",
> "chr1", "chr2", "chr2", "chr2"), start =
> c(2000010, 19000000, 30000000, 300, 5500, 100000),
> end = c(2000310, 19000300, 30000300, 600, 5800,
> 100300))
> featuresT <- data.frame(name = c("gene1", "gene2",
> "gene3", "gene4", "gene5", "gene6"), chr =
> c("chr1", "chr1", "chr1", "chr2", "chr2", "chr2"),
> start = c(1000000, 10000000, 15000000, 1000, 6000,
> 10000), end = c(2000000, 20000000, 22000000, 5000,
> 7000, 15000), strand = c('+', '-', '+', '+', '-',
> '+'))
>
> require(ChIPpeakAnno)
>
> peaksRangedData <- RangedData(space = peaksT$chr,
> ranges = IRanges(start = peaksT$start, end =
> peaksT$end))
> featuresRangedData <- RangedData(name =
> featuresT$name, space = featuresT$chr, strand =
> featuresT$strand, ranges = IRanges(start =
> featuresT$start, end = featuresT$end))
> featureLoc <- "TSS"
>
> annotatePeakInBatch(peaksRangedData,
> AnnotationData = featuresRangedData,
> PeakLocForDistance = "middle")
>
> Error in if (as.character(r.n$strand[i]) == "1" ||
> as.character(r.n$strand[i]) == :
> missing value where TRUE/FALSE needed
>
> My sessionInfo is :
>
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
>
> [3] LC_TIME=en_AU.UTF-8
> LC_COLLATE=en_AU.UTF-8
> [5] LC_MONETARY=C
> LC_MESSAGES=en_AU.UTF-8
> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_AU.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils
> datasets methods base
>
> other attached packages:
> [1] ChIPpeakAnno_1.5.2
> limma_3.4.0
>
> [3] org.Hs.eg.db_2.4.1
> GO.db_2.4.1
>
> [5] RSQLite_0.9-0 DBI_0.2-5
>
> [7] AnnotationDbi_1.10.0
> BSgenome.Ecoli.NCBI.20080805_1.3.16
> [9] BSgenome_1.16.1
> GenomicRanges_1.0.1
>
> [11] Biostrings_2.16.0
> IRanges_1.6.2
>
> [13] multtest_2.4.0
> Biobase_2.8.0
>
> [15] biomaRt_2.4.0
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-6 RCurl_1.4-2 splines_2.11.0
> survival_2.35-8
> [5] XML_3.1-0
>
> Thanks,
> Dario.
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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