TranscriptDb object to RangedData for ChIPpeakAnno
2
0
Entering edit mode
Alan Smith ▴ 150
@alan-smith-5987
Last seen 6.9 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 • 1.5k views
ADD COMMENT
0
Entering edit mode
Alan Smith ▴ 150
@alan-smith-5987
Last seen 6.9 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]]
ADD COMMENT
0
Entering edit mode
Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 1 day 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
ADD COMMENT
0
Entering edit mode
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]]
ADD REPLY

Login before adding your answer.

Traffic: 927 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6