TranscriptDb object to RangedData for ChIPpeakAnno
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Alan Smith ▴ 150
@alan-smith-5987
Last seen 4.4 years ago
United States
Hello All, I apologize if this email shows up twice to the mailing list. I'm trying to use ChIPpeakAnno to identify the annotation of ChIP-Seq peaks for an organism that does not have an annotation package. I have used makeTranscriptDbFromGFF to create a transcriptDb object and trying to pass it as the annotation data for annotatePeakInBatch function. However, I suppose it is not the way to handle that. I tried googling quite a bit but no luck. Is there a way to convert TranscriptDb object to RangedData? The error I ended up with: Error in annotatePeakInBatch(t.rangedData, AnnotationData = ep, : AnnotationData needs to be RangedData object Please let me know how to approach this issue. Thanks for any help. Alan Here is my code and sessionInfo: library(ChIPpeakAnno) test.rangedData = BED2RangedData("ChIP-test.bed") test.rangedData txdb <- makeTranscriptDbFromGFF(file="spgen.gtf", format="gtf", exonRankAttributeName="exon_number", dataSource=paste("eunam",sep=""), species="epp") saveDb(txdb,file="spgenGTF.sqlite") ep <- loadDb("spgenGTF.sqlite",) annotatedPeakEP= annotatePeakInBatch(test.rangedData, AnnotationData = ep, output="both", maxgap=1000, multiple=TRUE) Error in annotatePeakInBatch(test.rangedData, AnnotationData = ep, : AnnotationData needs to be RangedData object sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.20.4 ChIPpeakAnno_2.8.0 GenomicFeatures_1.12.2 limma_3.16.6 [5] org.Hs.eg.db_2.9.0 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 [9] AnnotationDbi_1.22.6 BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.28.0 GenomicRanges_1.12.4 [13] Biostrings_2.28.0 IRanges_1.18.2 multtest_2.16.0 Biobase_2.20.1 [17] biomaRt_2.16.0 BiocGenerics_0.6.0 VennDiagram_1.6.0 loaded via a namespace (and not attached): [1] bitops_1.0-5 MASS_7.3-27 RCurl_1.95-4.1 Rsamtools_1.12.3 splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 [9] XML_3.95-0.2 zlibbioc_1.6.0 [[alternative HTML version deleted]]
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno • 926 views
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Alan Smith ▴ 150
@alan-smith-5987
Last seen 4.4 years ago
United States
Hello All, I'm trying to use ChIPpeakAnno to identify the annotation of ChIP-Seq peaks for an organism that does not have an annotation package. I have used makeTranscriptDbFromGFF to create a transcriptDb object and trying to pass it as the annotation data for annotatePeakInBatch function. However, I suppose it is not the way to handle that. I tried googling quite a bit but no luck. Ended up getting this error: Error in annotatePeakInBatch(t.rangedData, AnnotationData = ep, : AnnotationData needs to be RangedData object Please let me know how to approach this issue. Thanks for any help. Alan Here is my code and sessionInfo: library(ChIPpeakAnno) test.rangedData = BED2RangedData("ChIP-test.bed") test.rangedData txdb <- makeTranscriptDbFromGFF(file="spgen.gtf", format="gtf", exonRankAttributeName="exon_number", dataSource=paste("eunam",sep=""), species="epp") saveDb(txdb,file="spgenGTF.sqlite") ep <- loadDb("spgenGTF.sqlite",) annotatedPeakEP= annotatePeakInBatch(test.rangedData, AnnotationData = ep, output="both", maxgap=1000, multiple=TRUE) Error in annotatePeakInBatch(test.rangedData, AnnotationData = ep, : AnnotationData needs to be RangedData object sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.20.4 ChIPpeakAnno_2.8.0 GenomicFeatures_1.12.2 limma_3.16.6 [5] org.Hs.eg.db_2.9.0 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 [9] AnnotationDbi_1.22.6 BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.28.0 GenomicRanges_1.12.4 [13] Biostrings_2.28.0 IRanges_1.18.2 multtest_2.16.0 Biobase_2.20.1 [17] biomaRt_2.16.0 BiocGenerics_0.6.0 VennDiagram_1.6.0 loaded via a namespace (and not attached): [1] bitops_1.0-5 MASS_7.3-27 RCurl_1.95-4.1 Rsamtools_1.12.3 splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 [9] XML_3.95-0.2 zlibbioc_1.6.0 [[alternative HTML version deleted]]
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 3 months ago
United States
Hi Alan, I think one way is that to create object Granges first and then convert it to RangedData use code like, exons <- exons(TranscriptDb, columns=NULL) introns <- unique(unlist(intronsByTranscript(TranscriptDb))) fiveUTRs <- unique(unlist(fiveUTRsByTranscript(TranscriptDb))) threeUTRs <- unique(unlist(threeUTRsByTranscript(TranscriptDb))) transcripts <- transcripts(TranscriptDb, columns=NULL) Hope this will help you. Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 7/18/13 3:39 PM, "Alan Smith" <alan.sm310 at="" gmail.com=""> wrote: >Hello All, > >I apologize if this email shows up twice to the mailing list. > >I'm trying to use ChIPpeakAnno to identify the annotation of ChIP-Seq >peaks >for an organism that does not have an annotation package. I have used >makeTranscriptDbFromGFF to create a transcriptDb object and trying to pass >it as the annotation data for annotatePeakInBatch function. However, I >suppose it is not the way to handle that. I tried googling quite a bit but >no luck. > >Is there a way to convert TranscriptDb object to RangedData? > >The error I ended up with: > >Error in annotatePeakInBatch(t.rangedData, AnnotationData = ep, : > AnnotationData needs to be RangedData object > >Please let me know how to approach this issue. >Thanks for any help. >Alan > >Here is my code and sessionInfo: > >library(ChIPpeakAnno) >test.rangedData = BED2RangedData("ChIP-test.bed") >test.rangedData >txdb <- makeTranscriptDbFromGFF(file="spgen.gtf", format="gtf", >exonRankAttributeName="exon_number", dataSource=paste("eunam",sep=""), >species="epp") >saveDb(txdb,file="spgenGTF.sqlite") >ep <- loadDb("spgenGTF.sqlite",) >annotatedPeakEP= annotatePeakInBatch(test.rangedData, AnnotationData = ep, >output="both", maxgap=1000, multiple=TRUE) > >Error in annotatePeakInBatch(test.rangedData, AnnotationData = ep, : > AnnotationData needs to be RangedData object > >sessionInfo() >R version 3.0.1 (2013-05-16) >Platform: x86_64-apple-darwin10.8.0 (64-bit) > >locale: >[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >attached base packages: >[1] parallel grid stats graphics grDevices utils datasets > methods base > >other attached packages: > [1] rtracklayer_1.20.4 ChIPpeakAnno_2.8.0 > GenomicFeatures_1.12.2 limma_3.16.6 > [5] org.Hs.eg.db_2.9.0 GO.db_2.9.0 > RSQLite_0.11.4 DBI_0.2-7 > [9] AnnotationDbi_1.22.6 > BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.28.0 >GenomicRanges_1.12.4 >[13] Biostrings_2.28.0 IRanges_1.18.2 > multtest_2.16.0 Biobase_2.20.1 >[17] biomaRt_2.16.0 BiocGenerics_0.6.0 > VennDiagram_1.6.0 > >loaded via a namespace (and not attached): > [1] bitops_1.0-5 MASS_7.3-27 RCurl_1.95-4.1 Rsamtools_1.12.3 >splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 > [9] XML_3.95-0.2 zlibbioc_1.6.0 > > [[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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Hello Jianhong, Thank you so much. It worked like a charm. regards, Alan On Thu, Jul 18, 2013 at 3:04 PM, Ou, Jianhong <jianhong.ou@umassmed.edu>wrote: > Hi Alan, > > I think one way is that to create object Granges first and then convert it > to RangedData use code like, > > exons <- exons(TranscriptDb, columns=NULL) > introns <- unique(unlist(intronsByTranscript(TranscriptDb))) > fiveUTRs <- unique(unlist(fiveUTRsByTranscript(TranscriptDb))) > threeUTRs <- unique(unlist(threeUTRsByTranscript(TranscriptDb))) > transcripts <- transcripts(TranscriptDb, columns=NULL) > > > Hope this will help you. > > Yours sincerely, > > Jianhong Ou > > LRB 670A > Program in Gene Function and Expression > 364 Plantation Street Worcester, > MA 01605 > > > > > On 7/18/13 3:39 PM, "Alan Smith" <alan.sm310@gmail.com> wrote: > > >Hello All, > > > >I apologize if this email shows up twice to the mailing list. > > > >I'm trying to use ChIPpeakAnno to identify the annotation of ChIP- Seq > >peaks > >for an organism that does not have an annotation package. I have used > >makeTranscriptDbFromGFF to create a transcriptDb object and trying to pass > >it as the annotation data for annotatePeakInBatch function. However, I > >suppose it is not the way to handle that. I tried googling quite a bit but > >no luck. > > > >Is there a way to convert TranscriptDb object to RangedData? > > > >The error I ended up with: > > > >Error in annotatePeakInBatch(t.rangedData, AnnotationData = ep, : > > AnnotationData needs to be RangedData object > > > >Please let me know how to approach this issue. > >Thanks for any help. > >Alan > > > >Here is my code and sessionInfo: > > > >library(ChIPpeakAnno) > >test.rangedData = BED2RangedData("ChIP-test.bed") > >test.rangedData > >txdb <- makeTranscriptDbFromGFF(file="spgen.gtf", format="gtf", > >exonRankAttributeName="exon_number", dataSource=paste("eunam",sep=""), > >species="epp") > >saveDb(txdb,file="spgenGTF.sqlite") > >ep <- loadDb("spgenGTF.sqlite",) > >annotatedPeakEP= annotatePeakInBatch(test.rangedData, AnnotationData = ep, > >output="both", maxgap=1000, multiple=TRUE) > > > >Error in annotatePeakInBatch(test.rangedData, AnnotationData = ep, : > > AnnotationData needs to be RangedData object > > > >sessionInfo() > >R version 3.0.1 (2013-05-16) > >Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > >locale: > >[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > >attached base packages: > >[1] parallel grid stats graphics grDevices utils datasets > > methods base > > > >other attached packages: > > [1] rtracklayer_1.20.4 ChIPpeakAnno_2.8.0 > > GenomicFeatures_1.12.2 limma_3.16.6 > > [5] org.Hs.eg.db_2.9.0 GO.db_2.9.0 > > RSQLite_0.11.4 DBI_0.2-7 > > [9] AnnotationDbi_1.22.6 > > BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.28.0 > >GenomicRanges_1.12.4 > >[13] Biostrings_2.28.0 IRanges_1.18.2 > > multtest_2.16.0 Biobase_2.20.1 > >[17] biomaRt_2.16.0 BiocGenerics_0.6.0 > > VennDiagram_1.6.0 > > > >loaded via a namespace (and not attached): > > [1] bitops_1.0-5 MASS_7.3-27 RCurl_1.95-4.1 Rsamtools_1.12.3 > >splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 > > [9] XML_3.95-0.2 zlibbioc_1.6.0 > > > > [[alternative HTML version deleted]] > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@r-project.org > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
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