ChIPpeakAnno problem w getAllPeakSequence()
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Anna ▴ 50
@anna-5560
Last seen 4.6 years ago
Sweden
Dear list, I've just started analyzing a ChIP-seq data set. I generated a peak list using "standard" utilities (bowtie, MACS) and loaded it into R in the ChIPpeakAnno package. I managed to annotate the peaks but when I tried to retrieve the peak sequences using the getAllPeakSequence() function I ran into a problem: peaksequences<-getAllPeakSequence(mergedpeakannotations, upstream=100, downstream=100, genome=mart, AnnotationData=getAnnotation(mart, featureType="TSS")) Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), : Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND The error message sometimes states downstream_flank instead of upstream. At one point I got it to run on a small subset of the data (first 10 rows) but later the same command failed with this same error message. Some info about the objects: mergedpeakannotations: RangedData object, created using mergedpeakannotations<- annotatePeakInBatch(mergedpeak.rd, AnnotationData=getAnnotation(mart, featureType="TSS")) mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") Anybody got a clue about why this fails? All help would be much appreciated! Best regards! Anna sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C [5] LC_TIME=Swedish_Sweden.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_2.6.0 limma_3.14.1 [3] org.Hs.eg.db_2.8.0 GO.db_2.8.0 [5] RSQLite_0.11.2 DBI_0.2-5 [7] AnnotationDbi_1.20.1 BSgenome.Ecoli.NCBI.20080805_1.3.17 [9] BSgenome_1.26.1 GenomicRanges_1.10.2 [11] Biostrings_2.26.2 IRanges_1.16.2 [13] multtest_2.14.0 Biobase_2.18.0 [15] biomaRt_2.14.0 BiocGenerics_0.4.0 [17] VennDiagram_1.5.1 loaded via a namespace (and not attached): [1] MASS_7.3-22 parallel_2.15.1 RCurl_1.95-1.1 splines_2.15.1 stats4_2.15.1 [6] survival_2.36-14 tools_2.15.1 XML_3.95-0.1 [[alternative HTML version deleted]]
GO annotate ChIPpeakAnno GO annotate ChIPpeakAnno • 907 views
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 3 days ago
United States
Hi Anna, To get the peak sequences you can try BSgenome + BStrings first. Try ?getSeq to extract the sequence from local database, faster than remote mart. Because I can not repeat your error, could you please share the subset of you data to me for testing? Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Oct 17, 2012, at 9:14 AM, Anna Ehrlund wrote: > Dear list, > > I've just started analyzing a ChIP-seq data set. I generated a peak list using "standard" utilities (bowtie, MACS) and loaded it into R in the ChIPpeakAnno package. I managed to annotate the peaks but when I tried to retrieve the peak sequences using the getAllPeakSequence() function I ran into a problem: > > > peaksequences<-getAllPeakSequence(mergedpeakannotations, upstream=100, downstream=100, genome=mart, AnnotationData=getAnnotation(mart, featureType="TSS")) > Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), : > Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND > > The error message sometimes states downstream_flank instead of upstream. At one point I got it to run on a small subset of the data (first 10 rows) but later the same command failed with this same error message. > > Some info about the objects: > mergedpeakannotations: RangedData object, created using mergedpeakannotations<- annotatePeakInBatch(mergedpeak.rd, AnnotationData=getAnnotation(mart, featureType="TSS")) > > mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") > > Anybody got a clue about why this fails? All help would be much appreciated! > > Best regards! > Anna > > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 > [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C > [5] LC_TIME=Swedish_Sweden.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPpeakAnno_2.6.0 limma_3.14.1 > [3] org.Hs.eg.db_2.8.0 GO.db_2.8.0 > [5] RSQLite_0.11.2 DBI_0.2-5 > [7] AnnotationDbi_1.20.1 BSgenome.Ecoli.NCBI.20080805_1.3.17 > [9] BSgenome_1.26.1 GenomicRanges_1.10.2 > [11] Biostrings_2.26.2 IRanges_1.16.2 > [13] multtest_2.14.0 Biobase_2.18.0 > [15] biomaRt_2.14.0 BiocGenerics_0.4.0 > [17] VennDiagram_1.5.1 > > loaded via a namespace (and not attached): > [1] MASS_7.3-22 parallel_2.15.1 RCurl_1.95-1.1 splines_2.15.1 stats4_2.15.1 > [6] survival_2.36-14 tools_2.15.1 XML_3.95-0.1 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Anna, And a better way to resolve your problem is that use BSgenome as annotationData for getAllPeakSequence() function. Try, library(BSgenome.Hsapiens.UCSC.hg19) peaksequences <- getAllPeakSequence(mergedpeakannotations, upstream=100, downstream=100, genome=Hsapiens) Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Oct 17, 2012, at 12:03 PM, wrote: > Hi Anna, > > To get the peak sequences you can try BSgenome + BStrings first. Try ?getSeq to extract the sequence from local database, faster than remote mart. > > Because I can not repeat your error, could you please share the subset of you data to me for testing? > > Yours sincerely, > > Jianhong Ou > > jianhong.ou at umassmed.edu > > > On Oct 17, 2012, at 9:14 AM, Anna Ehrlund wrote: > >> Dear list, >> >> I've just started analyzing a ChIP-seq data set. I generated a peak list using "standard" utilities (bowtie, MACS) and loaded it into R in the ChIPpeakAnno package. I managed to annotate the peaks but when I tried to retrieve the peak sequences using the getAllPeakSequence() function I ran into a problem: >> >> >> peaksequences<-getAllPeakSequence(mergedpeakannotations, upstream=100, downstream=100, genome=mart, AnnotationData=getAnnotation(mart, featureType="TSS")) >> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), : >> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND >> >> The error message sometimes states downstream_flank instead of upstream. At one point I got it to run on a small subset of the data (first 10 rows) but later the same command failed with this same error message. >> >> Some info about the objects: >> mergedpeakannotations: RangedData object, created using mergedpeakannotations<- annotatePeakInBatch(mergedpeak.rd, AnnotationData=getAnnotation(mart, featureType="TSS")) >> >> mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") >> >> Anybody got a clue about why this fails? All help would be much appreciated! >> >> Best regards! >> Anna >> >> >> >> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 >> [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C >> [5] LC_TIME=Swedish_Sweden.1252 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ChIPpeakAnno_2.6.0 limma_3.14.1 >> [3] org.Hs.eg.db_2.8.0 GO.db_2.8.0 >> [5] RSQLite_0.11.2 DBI_0.2-5 >> [7] AnnotationDbi_1.20.1 BSgenome.Ecoli.NCBI.20080805_1.3.17 >> [9] BSgenome_1.26.1 GenomicRanges_1.10.2 >> [11] Biostrings_2.26.2 IRanges_1.16.2 >> [13] multtest_2.14.0 Biobase_2.18.0 >> [15] biomaRt_2.14.0 BiocGenerics_0.4.0 >> [17] VennDiagram_1.5.1 >> >> loaded via a namespace (and not attached): >> [1] MASS_7.3-22 parallel_2.15.1 RCurl_1.95-1.1 splines_2.15.1 stats4_2.15.1 >> [6] survival_2.36-14 tools_2.15.1 XML_3.95-0.1 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi Jianhong, Thanks so much for your help, your suggestion to use the BSgenome as annotaionData worked perfectly. Problem solved for me. The bioMart-dependent code still fails on the same data set, not sure why, perhaps a glitch in my bioMart connection or something (no other network problems here though). I'll send you a subset of my data (that fails) off-list if you want to try and reproduce the problem. Again, thanks for your quick help! Anna ________________________________________ Fr?n: Ou, Jianhong [Jianhong.Ou at umassmed.edu] Skickat: den 17 oktober 2012 18:22 Till: Anna Ehrlund Cc: <bioconductor at="" r-project.org=""> ?mne: Re: [BioC] ChIPpeakAnno problem w getAllPeakSequence() Hi Anna, And a better way to resolve your problem is that use BSgenome as annotationData for getAllPeakSequence() function. Try, library(BSgenome.Hsapiens.UCSC.hg19) peaksequences <- getAllPeakSequence(mergedpeakannotations, upstream=100, downstream=100, genome=Hsapiens) Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Oct 17, 2012, at 12:03 PM, wrote: > Hi Anna, > > To get the peak sequences you can try BSgenome + BStrings first. Try ?getSeq to extract the sequence from local database, faster than remote mart. > > Because I can not repeat your error, could you please share the subset of you data to me for testing? > > Yours sincerely, > > Jianhong Ou > > jianhong.ou at umassmed.edu > > > On Oct 17, 2012, at 9:14 AM, Anna Ehrlund wrote: > >> Dear list, >> >> I've just started analyzing a ChIP-seq data set. I generated a peak list using "standard" utilities (bowtie, MACS) and loaded it into R in the ChIPpeakAnno package. I managed to annotate the peaks but when I tried to retrieve the peak sequences using the getAllPeakSequence() function I ran into a problem: >> >> >> peaksequences<-getAllPeakSequence(mergedpeakannotations, upstream=100, downstream=100, genome=mart, AnnotationData=getAnnotation(mart, featureType="TSS")) >> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), : >> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND >> >> The error message sometimes states downstream_flank instead of upstream. At one point I got it to run on a small subset of the data (first 10 rows) but later the same command failed with this same error message. >> >> Some info about the objects: >> mergedpeakannotations: RangedData object, created using mergedpeakannotations<- annotatePeakInBatch(mergedpeak.rd, AnnotationData=getAnnotation(mart, featureType="TSS")) >> >> mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") >> >> Anybody got a clue about why this fails? All help would be much appreciated! >> >> Best regards! >> Anna >> >> >> >> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 >> [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C >> [5] LC_TIME=Swedish_Sweden.1252 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ChIPpeakAnno_2.6.0 limma_3.14.1 >> [3] org.Hs.eg.db_2.8.0 GO.db_2.8.0 >> [5] RSQLite_0.11.2 DBI_0.2-5 >> [7] AnnotationDbi_1.20.1 BSgenome.Ecoli.NCBI.20080805_1.3.17 >> [9] BSgenome_1.26.1 GenomicRanges_1.10.2 >> [11] Biostrings_2.26.2 IRanges_1.16.2 >> [13] multtest_2.14.0 Biobase_2.18.0 >> [15] biomaRt_2.14.0 BiocGenerics_0.4.0 >> [17] VennDiagram_1.5.1 >> >> loaded via a namespace (and not attached): >> [1] MASS_7.3-22 parallel_2.15.1 RCurl_1.95-1.1 splines_2.15.1 stats4_2.15.1 >> [6] survival_2.36-14 tools_2.15.1 XML_3.95-0.1 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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