ChIPpeakAnno::getEnrichedGo crashes but I don't know why
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Eric Cabot ▴ 40
@eric-cabot-4419
Last seen 7.2 years ago
I am a relatively new Bioconductor user and I am trying to analyze some ChIP-seq results that came from QuEST using the ChIPpeakAnno package. After importing the regions of interest into RangedData objects and doing the following: ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_gene_ ensembl") ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, featureType="ExonPlusUtr") I had no problem annotating and generating a Venn diagram to show the overlaps between my three sets of peaks. To annotate, I used: annotated_regions=annotatePeakInBatch(myranged, AnnotationData=ENSEMBL_ExonPlus_Annotation) But I cannot seem to get the getEnrichedGo method to work on this (or my other two annotated regions). Here is a typical command line: my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",m axP=0.01,multiAdj=TRUE,minGOterm=1, multiAdjMethod="BH",feature_id_type="ensembl_gene_id") and here is a typical error message: enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",maxP =0.01,multiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : argument is of length zero Which leads me to ask: 1) Is this error message supposed to be meaningful to me-i.e. a user- or is it something that I should be sending to the developer of the package? 2) Is there anything obvious from this that suggests what corrective action I should be taking? Eric Cabot University of Wisconsin
annotate ChIPpeakAnno annotate ChIPpeakAnno • 1.4k views
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Julie Zhu ★ 4.3k
@julie-zhu-3596
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Hi Eric, Could you please post the session information with sessionInfo() command? Could you please also send a few ensembl IDs in your annotated dataset? Thanks! Best regards, Julie On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: > I am a relatively new Bioconductor user and I am trying to analyze some > ChIP-seq results that came from QuEST using the ChIPpeakAnno package. > > After importing the regions of interest into RangedData objects and doing > the following: > > ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_gene_ ensembl"> ) > ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, > featureType="ExonPlusUtr") > > > I had no problem annotating and generating a Venn diagram to show the > overlaps between my three sets of peaks. To annotate, I used: > > annotated_regions=annotatePeakInBatch(myranged, > AnnotationData=ENSEMBL_ExonPlus_Annotation) > > > But I cannot seem to get the getEnrichedGo method to work on this (or my > other two annotated regions). Here is a typical command line: > > > my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db" ,maxP=0.01 > ,multiAdj=TRUE,minGOterm=1, > multiAdjMethod="BH",feature_id_type="ensembl_gene_id") > > and here is a typical error message: > > enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",ma xP=0.01,mu > ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") > Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : > argument is of length zero > > > Which leads me to ask: > > 1) Is this error message supposed to be meaningful to me-i.e. a user-or is > it something that I should be sending to the developer of the package? > > 2) Is there anything obvious from this that suggests what corrective > action I should be taking? > > > Eric Cabot > University of Wisconsin > > _______________________________________________ > 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 Julie, Thank you for your response. Here is the sessionInfo and traceback output and also a few lines of "my_annotated_regions". Regards, Eric Cabot > sessionInfo() R version 2.12.1 (2010-12-16) 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 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.6.0 limma_3.6.9 [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [5] RSQLite_0.9-4 DBI_0.2-5 [7] AnnotationDbi_1.12.0 BSgenome.Ecoli.NCBI.20080805_1.3.16 [9] BSgenome_1.18.2 GenomicRanges_1.2.2 [11] Biostrings_2.18.2 IRanges_1.8.8 [13] multtest_2.6.0 Biobase_2.10.0 [15] biomaRt_2.6.0 loaded via a namespace (and not attached): [1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2 [5] tools_2.12.1 XML_3.2-0 > my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs.eg.db ",maxP=0.01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_i d") Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : argument is of length zero > traceback() 2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp") 1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db", maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type = "ensembl_gene_id") > as.data.frame(my_annotated_regions[1:15,]) space start end width names peak strand 1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 + 2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 + 3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 + 4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 + 5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 + 6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 + 7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 + 8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 + 9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 + 10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 + 11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 + 12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 + 13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 + 14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 + 15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 + feature start_position end_position insideFeature distancetoFeature 1 ENSE00001749374 241995237 241996089 downstream 2699 2 ENSE00001643382 237144639 237145008 upstream -34896 3 ENSE00001807176 236078715 236078821 downstream 1552 4 ENSE00001776382 233807017 233807237 downstream 46228 5 ENSE00001442190 233749750 233750272 upstream -21794 6 ENSE00001731401 230728406 230728586 overlapEnd 148 7 ENSE00001439385 229685652 229685769 downstream 1477 8 ENSE00001903546 228882063 228882416 downstream 61200 9 ENSE00001439386 218303137 218303294 downstream 55748 10 ENSE00001624346 212253973 212254092 downstream 286 11 ENSE00001903225 210111538 210111622 upstream -25274 12 ENSE00001336255 209859550 209859630 downstream 3999 13 ENSE00001742112 207438342 207438381 upstream -1225 14 ENSE00001782518 190331193 190331400 downstream 21207 15 ENSE00001283926 184446520 184446737 upstream -13913 shortestDistance fromOverlappingOrNearest 1 1847 NearestStart 2 34637 NearestStart 3 1446 NearestStart 4 46008 NearestStart 5 21646 NearestStart 6 32 NearestStart 7 1360 NearestStart 8 60847 NearestStart 9 55591 NearestStart 10 167 NearestStart 11 25025 NearestStart 12 3919 NearestStart 13 1078 NearestStart 14 21000 NearestStart 15 13765 NearestStart Zhu, Lihua (Julie) wrote: > Hi Eric, > > Could you please post the session information with sessionInfo() command? > Could you please also send a few ensembl IDs in your annotated dataset? > Thanks! > > Best regards, > > Julie > > > On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: > >> I am a relatively new Bioconductor user and I am trying to analyze some >> ChIP-seq results that came from QuEST using the ChIPpeakAnno package. >> >> After importing the regions of interest into RangedData objects and doing >> the following: >> >> > ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_gen e_ensembl"> > ) >> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, >> featureType="ExonPlusUtr") >> >> >> I had no problem annotating and generating a Venn diagram to show the >> overlaps between my three sets of peaks. To annotate, I used: >> >> annotated_regions=annotatePeakInBatch(myranged, >> AnnotationData=ENSEMBL_ExonPlus_Annotation) >> >> >> But I cannot seem to get the getEnrichedGo method to work on this (or my >> other two annotated regions). Here is a typical command line: >> >> >> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db ",maxP=0.01 >> ,multiAdj=TRUE,minGOterm=1, >> multiAdjMethod="BH",feature_id_type="ensembl_gene_id") >> >> and here is a typical error message: >> >> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",m axP=0.01,mu >> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") >> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >> argument is of length zero >> >> >> Which leads me to ask: >> >> 1) Is this error message supposed to be meaningful to me-i.e. a user-or is >> it something that I should be sending to the developer of the package? >> >> 2) Is there anything obvious from this that suggests what corrective >> action I should be taking? >> >> >> Eric Cabot >> University of Wisconsin >> >> _______________________________________________ >> 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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Eric, The annotated dataset has exon ID instead of gene ID while the getEnrichedGO is expecting feature_id_type="ensembl_gene_id". For a list of supported feature_id_type, please type ?getEnrichedGO. To use getEnrichedGO function, first get the TSS annotation. TSS.human.NCBI36 = getAnnotation(ENSEMBLE_GENES_MART, featureType="TSS") or use the build in TSS as data(TSS.human.NCBI36) Then annotate your peaks with TSS.human.NCBI36 followed by getEnrichedGO call. Please let me know if this works for you. Best regards, Julie On 1/5/11 12:29 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: > Hi Julie, > > Thank you for your response. > > Here is the sessionInfo and traceback output and also a few lines of > "my_annotated_regions". > > Regards, > > Eric Cabot > >> sessionInfo() > R version 2.12.1 (2010-12-16) > 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 > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPpeakAnno_1.6.0 limma_3.6.9 > [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 > [5] RSQLite_0.9-4 DBI_0.2-5 > [7] AnnotationDbi_1.12.0 BSgenome.Ecoli.NCBI.20080805_1.3.16 > [9] BSgenome_1.18.2 GenomicRanges_1.2.2 > [11] Biostrings_2.18.2 IRanges_1.8.8 > [13] multtest_2.6.0 Biobase_2.10.0 > [15] biomaRt_2.6.0 > > loaded via a namespace (and not attached): > [1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2 > [5] tools_2.12.1 XML_3.2-0 >> > my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs.eg. db",maxP=0 > .01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_id") > Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : > argument is of length zero >> traceback() > 2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp") > 1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db", > maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type = > "ensembl_gene_id") > > > >> as.data.frame(my_annotated_regions[1:15,]) > space start end width names peak strand > 1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 + > 2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 + > 3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 + > 4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 + > 5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 + > 6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 + > 7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 + > 8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 + > 9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 + > 10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 + > 11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 + > 12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 + > 13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 + > 14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 + > 15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 + > feature start_position end_position insideFeature > distancetoFeature > 1 ENSE00001749374 241995237 241996089 downstream 2699 > 2 ENSE00001643382 237144639 237145008 upstream -34896 > 3 ENSE00001807176 236078715 236078821 downstream 1552 > 4 ENSE00001776382 233807017 233807237 downstream 46228 > 5 ENSE00001442190 233749750 233750272 upstream -21794 > 6 ENSE00001731401 230728406 230728586 overlapEnd 148 > 7 ENSE00001439385 229685652 229685769 downstream 1477 > 8 ENSE00001903546 228882063 228882416 downstream 61200 > 9 ENSE00001439386 218303137 218303294 downstream 55748 > 10 ENSE00001624346 212253973 212254092 downstream 286 > 11 ENSE00001903225 210111538 210111622 upstream -25274 > 12 ENSE00001336255 209859550 209859630 downstream 3999 > 13 ENSE00001742112 207438342 207438381 upstream -1225 > 14 ENSE00001782518 190331193 190331400 downstream 21207 > 15 ENSE00001283926 184446520 184446737 upstream -13913 > shortestDistance fromOverlappingOrNearest > 1 1847 NearestStart > 2 34637 NearestStart > 3 1446 NearestStart > 4 46008 NearestStart > 5 21646 NearestStart > 6 32 NearestStart > 7 1360 NearestStart > 8 60847 NearestStart > 9 55591 NearestStart > 10 167 NearestStart > 11 25025 NearestStart > 12 3919 NearestStart > 13 1078 NearestStart > 14 21000 NearestStart > 15 13765 NearestStart > > > Zhu, Lihua (Julie) wrote: >> Hi Eric, >> >> Could you please post the session information with sessionInfo() command? >> Could you please also send a few ensembl IDs in your annotated dataset? >> Thanks! >> >> Best regards, >> >> Julie >> >> >> On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >> >>> I am a relatively new Bioconductor user and I am trying to analyze some >>> ChIP-seq results that came from QuEST using the ChIPpeakAnno package. >>> >>> After importing the regions of interest into RangedData objects and doing >>> the following: >>> >>> >> ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_ge ne_ensembl >> "> >> ) >>> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, >>> featureType="ExonPlusUtr") >>> >>> >>> I had no problem annotating and generating a Venn diagram to show the >>> overlaps between my three sets of peaks. To annotate, I used: >>> >>> annotated_regions=annotatePeakInBatch(myranged, >>> AnnotationData=ENSEMBL_ExonPlus_Annotation) >>> >>> >>> But I cannot seem to get the getEnrichedGo method to work on this (or my >>> other two annotated regions). Here is a typical command line: >>> >>> >>> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.d b",maxP=0. >>> 01 >>> ,multiAdj=TRUE,minGOterm=1, >>> multiAdjMethod="BH",feature_id_type="ensembl_gene_id") >>> >>> and here is a typical error message: >>> >>> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db", maxP=0.01, >>> mu >>> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") >>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>> argument is of length zero >>> >>> >>> Which leads me to ask: >>> >>> 1) Is this error message supposed to be meaningful to me-i.e. a user-or is >>> it something that I should be sending to the developer of the package? >>> >>> 2) Is there anything obvious from this that suggests what corrective >>> action I should be taking? >>> >>> >>> Eric Cabot >>> University of Wisconsin >>> >>> _______________________________________________ >>> 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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Julie Zhu ★ 4.3k
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Eric, You could convert the exon IDs associated with the peaks to ensemble gene IDs and input these ensemble gene IDs to the getEnrichedGO function. Best regards, Julie On 1/5/11 4:09 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: > Hi Julie, > > It may be a while before I get back to you on this, because I did my > mapping and ChIP-Seq analysis with Hg19 (NCBI 37), not Hg18 (NCBI 36). > I'm also a little concerned about using transcription start site > annotations rather than exons, because the the binding domains are not > thought to be restricted to only promoters. Any suggestions? > > Eric > > > > Zhu, Lihua (Julie) wrote: >> Eric, >> >> The annotated dataset has exon ID instead of gene ID while the getEnrichedGO >> is expecting feature_id_type="ensembl_gene_id". For a list of supported >> feature_id_type, please type ?getEnrichedGO. >> >> To use getEnrichedGO function, first get the TSS annotation. >> >> TSS.human.NCBI36 = getAnnotation(ENSEMBLE_GENES_MART, featureType="TSS") >> >> or use the build in TSS as >> >> data(TSS.human.NCBI36) >> >> Then annotate your peaks with TSS.human.NCBI36 followed by getEnrichedGO >> call. >> >> Please let me know if this works for you. >> >> Best regards, >> >> Julie >> >> >> >> >> On 1/5/11 12:29 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >> >>> Hi Julie, >>> >>> Thank you for your response. >>> >>> Here is the sessionInfo and traceback output and also a few lines of >>> "my_annotated_regions". >>> >>> Regards, >>> >>> Eric Cabot >>> >>>> sessionInfo() >>> R version 2.12.1 (2010-12-16) >>> 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 >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] ChIPpeakAnno_1.6.0 limma_3.6.9 >>> [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 >>> [5] RSQLite_0.9-4 DBI_0.2-5 >>> [7] AnnotationDbi_1.12.0 >>> BSgenome.Ecoli.NCBI.20080805_1.3.16 >>> [9] BSgenome_1.18.2 GenomicRanges_1.2.2 >>> [11] Biostrings_2.18.2 IRanges_1.8.8 >>> [13] multtest_2.6.0 Biobase_2.10.0 >>> [15] biomaRt_2.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2 >>> [5] tools_2.12.1 XML_3.2-0 >>> my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs.e g.db",maxP >>> =0 >>> .01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_id") >>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>> argument is of length zero >>>> traceback() >>> 2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp") >>> 1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db", >>> maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type = >>> "ensembl_gene_id") >>> >>> >>> >>>> as.data.frame(my_annotated_regions[1:15,]) >>> space start end width names peak strand >>> 1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 + >>> 2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 + >>> 3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 + >>> 4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 + >>> 5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 + >>> 6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 + >>> 7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 + >>> 8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 + >>> 9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 + >>> 10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 + >>> 11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 + >>> 12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 + >>> 13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 + >>> 14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 + >>> 15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 + >>> feature start_position end_position insideFeature >>> distancetoFeature >>> 1 ENSE00001749374 241995237 241996089 downstream >>> 2699 >>> 2 ENSE00001643382 237144639 237145008 upstream >>> -34896 >>> 3 ENSE00001807176 236078715 236078821 downstream >>> 1552 >>> 4 ENSE00001776382 233807017 233807237 downstream >>> 46228 >>> 5 ENSE00001442190 233749750 233750272 upstream >>> -21794 >>> 6 ENSE00001731401 230728406 230728586 overlapEnd >>> 148 >>> 7 ENSE00001439385 229685652 229685769 downstream >>> 1477 >>> 8 ENSE00001903546 228882063 228882416 downstream >>> 61200 >>> 9 ENSE00001439386 218303137 218303294 downstream >>> 55748 >>> 10 ENSE00001624346 212253973 212254092 downstream >>> 286 >>> 11 ENSE00001903225 210111538 210111622 upstream >>> -25274 >>> 12 ENSE00001336255 209859550 209859630 downstream >>> 3999 >>> 13 ENSE00001742112 207438342 207438381 upstream >>> -1225 >>> 14 ENSE00001782518 190331193 190331400 downstream >>> 21207 >>> 15 ENSE00001283926 184446520 184446737 upstream >>> -13913 >>> shortestDistance fromOverlappingOrNearest >>> 1 1847 NearestStart >>> 2 34637 NearestStart >>> 3 1446 NearestStart >>> 4 46008 NearestStart >>> 5 21646 NearestStart >>> 6 32 NearestStart >>> 7 1360 NearestStart >>> 8 60847 NearestStart >>> 9 55591 NearestStart >>> 10 167 NearestStart >>> 11 25025 NearestStart >>> 12 3919 NearestStart >>> 13 1078 NearestStart >>> 14 21000 NearestStart >>> 15 13765 NearestStart >>> >>> >>> Zhu, Lihua (Julie) wrote: >>>> Hi Eric, >>>> >>>> Could you please post the session information with sessionInfo() command? >>>> Could you please also send a few ensembl IDs in your annotated dataset? >>>> Thanks! >>>> >>>> Best regards, >>>> >>>> Julie >>>> >>>> >>>> On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >>>> >>>>> I am a relatively new Bioconductor user and I am trying to analyze some >>>>> ChIP-seq results that came from QuEST using the ChIPpeakAnno package. >>>>> >>>>> After importing the regions of interest into RangedData objects and doing >>>>> the following: >>>>> >>>>> >>>> ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_ gene_ensem >>>> bl >>>> "> >>>> ) >>>>> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, >>>>> featureType="ExonPlusUtr") >>>>> >>>>> >>>>> I had no problem annotating and generating a Venn diagram to show the >>>>> overlaps between my three sets of peaks. To annotate, I used: >>>>> >>>>> annotated_regions=annotatePeakInBatch(myranged, >>>>> AnnotationData=ENSEMBL_ExonPlus_Annotation) >>>>> >>>>> >>>>> But I cannot seem to get the getEnrichedGo method to work on this (or my >>>>> other two annotated regions). Here is a typical command line: >>>>> >>>>> >>>>> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg .db",maxP= >>>>> 0. >>>>> 01 >>>>> ,multiAdj=TRUE,minGOterm=1, >>>>> multiAdjMethod="BH",feature_id_type="ensembl_gene_id") >>>>> >>>>> and here is a typical error message: >>>>> >>>>> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db ",maxP=0.0 >>>>> 1, >>>>> mu >>>>> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") >>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>>>> argument is of length zero >>>>> >>>>> >>>>> Which leads me to ask: >>>>> >>>>> 1) Is this error message supposed to be meaningful to me-i.e. a user-or is >>>>> it something that I should be sending to the developer of the package? >>>>> >>>>> 2) Is there anything obvious from this that suggests what corrective >>>>> action I should be taking? >>>>> >>>>> >>>>> Eric Cabot >>>>> University of Wisconsin >>>>> >>>>> _______________________________________________ >>>>> 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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Julie, I don't know how to do that in R. I guess I can always export the annotations, do the association in Perl and re-import them as a vector to use with getEnrichedGo. Eric Zhu, Lihua (Julie) wrote: > Eric, > > You could convert the exon IDs associated with the peaks to ensemble gene > IDs and input these ensemble gene IDs to the getEnrichedGO function. > > Best regards, > > Julie > > > On 1/5/11 4:09 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: > >> Hi Julie, >> >> It may be a while before I get back to you on this, because I did my >> mapping and ChIP-Seq analysis with Hg19 (NCBI 37), not Hg18 (NCBI 36). >> I'm also a little concerned about using transcription start site >> annotations rather than exons, because the the binding domains are not >> thought to be restricted to only promoters. Any suggestions? >> >> Eric >> >> >> >> Zhu, Lihua (Julie) wrote: >>> Eric, >>> >>> The annotated dataset has exon ID instead of gene ID while the getEnrichedGO >>> is expecting feature_id_type="ensembl_gene_id". For a list of supported >>> feature_id_type, please type ?getEnrichedGO. >>> >>> To use getEnrichedGO function, first get the TSS annotation. >>> >>> TSS.human.NCBI36 = getAnnotation(ENSEMBLE_GENES_MART, featureType="TSS") >>> >>> or use the build in TSS as >>> >>> data(TSS.human.NCBI36) >>> >>> Then annotate your peaks with TSS.human.NCBI36 followed by getEnrichedGO >>> call. >>> >>> Please let me know if this works for you. >>> >>> Best regards, >>> >>> Julie >>> >>> >>> >>> >>> On 1/5/11 12:29 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >>> >>>> Hi Julie, >>>> >>>> Thank you for your response. >>>> >>>> Here is the sessionInfo and traceback output and also a few lines of >>>> "my_annotated_regions". >>>> >>>> Regards, >>>> >>>> Eric Cabot >>>> >>>>> sessionInfo() >>>> R version 2.12.1 (2010-12-16) >>>> 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 >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] ChIPpeakAnno_1.6.0 limma_3.6.9 >>>> [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 >>>> [5] RSQLite_0.9-4 DBI_0.2-5 >>>> [7] AnnotationDbi_1.12.0 >>>> BSgenome.Ecoli.NCBI.20080805_1.3.16 >>>> [9] BSgenome_1.18.2 GenomicRanges_1.2.2 >>>> [11] Biostrings_2.18.2 IRanges_1.8.8 >>>> [13] multtest_2.6.0 Biobase_2.10.0 >>>> [15] biomaRt_2.6.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2 >>>> [5] tools_2.12.1 XML_3.2-0 >>>> my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs. eg.db",maxP >>>> =0 >>>> .01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_id") >>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>>> argument is of length zero >>>>> traceback() >>>> 2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp") >>>> 1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db", >>>> maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type = >>>> "ensembl_gene_id") >>>> >>>> >>>> >>>>> as.data.frame(my_annotated_regions[1:15,]) >>>> space start end width names peak strand >>>> 1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 + >>>> 2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 + >>>> 3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 + >>>> 4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 + >>>> 5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 + >>>> 6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 + >>>> 7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 + >>>> 8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 + >>>> 9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 + >>>> 10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 + >>>> 11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 + >>>> 12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 + >>>> 13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 + >>>> 14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 + >>>> 15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 + >>>> feature start_position end_position insideFeature >>>> distancetoFeature >>>> 1 ENSE00001749374 241995237 241996089 downstream >>>> 2699 >>>> 2 ENSE00001643382 237144639 237145008 upstream >>>> -34896 >>>> 3 ENSE00001807176 236078715 236078821 downstream >>>> 1552 >>>> 4 ENSE00001776382 233807017 233807237 downstream >>>> 46228 >>>> 5 ENSE00001442190 233749750 233750272 upstream >>>> -21794 >>>> 6 ENSE00001731401 230728406 230728586 overlapEnd >>>> 148 >>>> 7 ENSE00001439385 229685652 229685769 downstream >>>> 1477 >>>> 8 ENSE00001903546 228882063 228882416 downstream >>>> 61200 >>>> 9 ENSE00001439386 218303137 218303294 downstream >>>> 55748 >>>> 10 ENSE00001624346 212253973 212254092 downstream >>>> 286 >>>> 11 ENSE00001903225 210111538 210111622 upstream >>>> -25274 >>>> 12 ENSE00001336255 209859550 209859630 downstream >>>> 3999 >>>> 13 ENSE00001742112 207438342 207438381 upstream >>>> -1225 >>>> 14 ENSE00001782518 190331193 190331400 downstream >>>> 21207 >>>> 15 ENSE00001283926 184446520 184446737 upstream >>>> -13913 >>>> shortestDistance fromOverlappingOrNearest >>>> 1 1847 NearestStart >>>> 2 34637 NearestStart >>>> 3 1446 NearestStart >>>> 4 46008 NearestStart >>>> 5 21646 NearestStart >>>> 6 32 NearestStart >>>> 7 1360 NearestStart >>>> 8 60847 NearestStart >>>> 9 55591 NearestStart >>>> 10 167 NearestStart >>>> 11 25025 NearestStart >>>> 12 3919 NearestStart >>>> 13 1078 NearestStart >>>> 14 21000 NearestStart >>>> 15 13765 NearestStart >>>> >>>> >>>> Zhu, Lihua (Julie) wrote: >>>>> Hi Eric, >>>>> >>>>> Could you please post the session information with sessionInfo() command? >>>>> Could you please also send a few ensembl IDs in your annotated dataset? >>>>> Thanks! >>>>> >>>>> Best regards, >>>>> >>>>> Julie >>>>> >>>>> >>>>> On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >>>>> >>>>>> I am a relatively new Bioconductor user and I am trying to analyze some >>>>>> ChIP-seq results that came from QuEST using the ChIPpeakAnno package. >>>>>> >>>>>> After importing the regions of interest into RangedData objects and doing >>>>>> the following: >>>>>> >>>>>> >>>>> ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens _gene_ensem >>>>> bl >>>>> "> >>>>> ) >>>>>> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, >>>>>> featureType="ExonPlusUtr") >>>>>> >>>>>> >>>>>> I had no problem annotating and generating a Venn diagram to show the >>>>>> overlaps between my three sets of peaks. To annotate, I used: >>>>>> >>>>>> annotated_regions=annotatePeakInBatch(myranged, >>>>>> AnnotationData=ENSEMBL_ExonPlus_Annotation) >>>>>> >>>>>> >>>>>> But I cannot seem to get the getEnrichedGo method to work on this (or my >>>>>> other two annotated regions). Here is a typical command line: >>>>>> >>>>>> >>>>>> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.e g.db",maxP= >>>>>> 0. >>>>>> 01 >>>>>> ,multiAdj=TRUE,minGOterm=1, >>>>>> multiAdjMethod="BH",feature_id_type="ensembl_gene_id") >>>>>> >>>>>> and here is a typical error message: >>>>>> >>>>>> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.d b",maxP=0.0 >>>>>> 1, >>>>>> mu >>>>>> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") >>>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>>>>> argument is of length zero >>>>>> >>>>>> >>>>>> Which leads me to ask: >>>>>> >>>>>> 1) Is this error message supposed to be meaningful to me-i.e. a user-or is >>>>>> it something that I should be sending to the developer of the package? >>>>>> >>>>>> 2) Is there anything obvious from this that suggests what corrective >>>>>> action I should be taking? >>>>>> >>>>>> >>>>>> Eric Cabot >>>>>> University of Wisconsin >>>>>> >>>>>> _______________________________________________ >>>>>> 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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Julie, In the end, I did a quick detour through Perl and getEnrichedGo worked as expected. Thanks for the help. Eric Eric Cabot wrote: > Julie, > > I don't know how to do that in R. I guess I can always export the > annotations, do the association in Perl and re-import them as a vector > to use with getEnrichedGo. > > Eric > > Zhu, Lihua (Julie) wrote: >> Eric, >> >> You could convert the exon IDs associated with the peaks to ensemble gene >> IDs and input these ensemble gene IDs to the getEnrichedGO function. >> >> Best regards, >> >> Julie >> >> >> On 1/5/11 4:09 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >> >>> Hi Julie, >>> >>> It may be a while before I get back to you on this, because I did my >>> mapping and ChIP-Seq analysis with Hg19 (NCBI 37), not Hg18 (NCBI 36). >>> I'm also a little concerned about using transcription start site >>> annotations rather than exons, because the the binding domains are not >>> thought to be restricted to only promoters. Any suggestions? >>> >>> Eric >>> >>> >>> >>> Zhu, Lihua (Julie) wrote: >>>> Eric, >>>> >>>> The annotated dataset has exon ID instead of gene ID while the >>>> getEnrichedGO >>>> is expecting feature_id_type="ensembl_gene_id". For a list of supported >>>> feature_id_type, please type ?getEnrichedGO. >>>> >>>> To use getEnrichedGO function, first get the TSS annotation. >>>> >>>> TSS.human.NCBI36 = getAnnotation(ENSEMBLE_GENES_MART, >>>> featureType="TSS") >>>> >>>> or use the build in TSS as >>>> >>>> data(TSS.human.NCBI36) >>>> >>>> Then annotate your peaks with TSS.human.NCBI36 followed by >>>> getEnrichedGO >>>> call. >>>> >>>> Please let me know if this works for you. >>>> >>>> Best regards, >>>> >>>> Julie >>>> >>>> >>>> >>>> >>>> On 1/5/11 12:29 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >>>> >>>>> Hi Julie, >>>>> >>>>> Thank you for your response. >>>>> >>>>> Here is the sessionInfo and traceback output and also a few lines of >>>>> "my_annotated_regions". >>>>> >>>>> Regards, >>>>> >>>>> Eric Cabot >>>>> >>>>>> sessionInfo() >>>>> R version 2.12.1 (2010-12-16) >>>>> 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 >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] ChIPpeakAnno_1.6.0 limma_3.6.9 >>>>> [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 >>>>> [5] RSQLite_0.9-4 DBI_0.2-5 >>>>> [7] AnnotationDbi_1.12.0 >>>>> BSgenome.Ecoli.NCBI.20080805_1.3.16 >>>>> [9] BSgenome_1.18.2 GenomicRanges_1.2.2 >>>>> [11] Biostrings_2.18.2 IRanges_1.8.8 >>>>> [13] multtest_2.6.0 Biobase_2.10.0 >>>>> [15] biomaRt_2.6.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2 >>>>> [5] tools_2.12.1 XML_3.2-0 >>>>> my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs .eg.db",maxP >>>>> >>>>> =0 >>>>> .01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_id") >>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>>>> argument is of length zero >>>>>> traceback() >>>>> 2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp") >>>>> 1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db", >>>>> maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type = >>>>> "ensembl_gene_id") >>>>> >>>>> >>>>> >>>>>> as.data.frame(my_annotated_regions[1:15,]) >>>>> space start end width names peak strand >>>>> 1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 + >>>>> 2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 + >>>>> 3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 + >>>>> 4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 + >>>>> 5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 + >>>>> 6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 + >>>>> 7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 + >>>>> 8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 + >>>>> 9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 + >>>>> 10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 + >>>>> 11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 + >>>>> 12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 + >>>>> 13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 + >>>>> 14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 + >>>>> 15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 + >>>>> feature start_position end_position insideFeature >>>>> distancetoFeature >>>>> 1 ENSE00001749374 241995237 241996089 downstream >>>>> 2699 >>>>> 2 ENSE00001643382 237144639 237145008 upstream >>>>> -34896 >>>>> 3 ENSE00001807176 236078715 236078821 downstream >>>>> 1552 >>>>> 4 ENSE00001776382 233807017 233807237 downstream >>>>> 46228 >>>>> 5 ENSE00001442190 233749750 233750272 upstream >>>>> -21794 >>>>> 6 ENSE00001731401 230728406 230728586 overlapEnd >>>>> 148 >>>>> 7 ENSE00001439385 229685652 229685769 downstream >>>>> 1477 >>>>> 8 ENSE00001903546 228882063 228882416 downstream >>>>> 61200 >>>>> 9 ENSE00001439386 218303137 218303294 downstream >>>>> 55748 >>>>> 10 ENSE00001624346 212253973 212254092 downstream >>>>> 286 >>>>> 11 ENSE00001903225 210111538 210111622 upstream >>>>> -25274 >>>>> 12 ENSE00001336255 209859550 209859630 downstream >>>>> 3999 >>>>> 13 ENSE00001742112 207438342 207438381 upstream >>>>> -1225 >>>>> 14 ENSE00001782518 190331193 190331400 downstream >>>>> 21207 >>>>> 15 ENSE00001283926 184446520 184446737 upstream >>>>> -13913 >>>>> shortestDistance fromOverlappingOrNearest >>>>> 1 1847 NearestStart >>>>> 2 34637 NearestStart >>>>> 3 1446 NearestStart >>>>> 4 46008 NearestStart >>>>> 5 21646 NearestStart >>>>> 6 32 NearestStart >>>>> 7 1360 NearestStart >>>>> 8 60847 NearestStart >>>>> 9 55591 NearestStart >>>>> 10 167 NearestStart >>>>> 11 25025 NearestStart >>>>> 12 3919 NearestStart >>>>> 13 1078 NearestStart >>>>> 14 21000 NearestStart >>>>> 15 13765 NearestStart >>>>> >>>>> >>>>> Zhu, Lihua (Julie) wrote: >>>>>> Hi Eric, >>>>>> >>>>>> Could you please post the session information with sessionInfo() >>>>>> command? >>>>>> Could you please also send a few ensembl IDs in your annotated >>>>>> dataset? >>>>>> Thanks! >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Julie >>>>>> >>>>>> >>>>>> On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >>>>>> >>>>>>> I am a relatively new Bioconductor user and I am trying to >>>>>>> analyze some >>>>>>> ChIP-seq results that came from QuEST using the ChIPpeakAnno >>>>>>> package. >>>>>>> >>>>>>> After importing the regions of interest into RangedData objects >>>>>>> and doing >>>>>>> the following: >>>>>>> >>>>>>> >>>>>> ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapien s_gene_ensem >>>>>> >>>>>> bl >>>>>> "> >>>>>> ) >>>>>>> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, >>>>>>> featureType="ExonPlusUtr") >>>>>>> >>>>>>> >>>>>>> I had no problem annotating and generating a Venn diagram to show >>>>>>> the >>>>>>> overlaps between my three sets of peaks. To annotate, I used: >>>>>>> >>>>>>> annotated_regions=annotatePeakInBatch(myranged, >>>>>>> AnnotationData=ENSEMBL_ExonPlus_Annotation) >>>>>>> >>>>>>> >>>>>>> But I cannot seem to get the getEnrichedGo method to work on this >>>>>>> (or my >>>>>>> other two annotated regions). Here is a typical command line: >>>>>>> >>>>>>> >>>>>>> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs. eg.db",maxP= >>>>>>> >>>>>>> 0. >>>>>>> 01 >>>>>>> ,multiAdj=TRUE,minGOterm=1, >>>>>>> multiAdjMethod="BH",feature_id_type="ensembl_gene_id") >>>>>>> >>>>>>> and here is a typical error message: >>>>>>> >>>>>>> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg. db",maxP=0.0 >>>>>>> >>>>>>> 1, >>>>>>> mu >>>>>>> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") >>>>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>>>>>> argument is of length zero >>>>>>> >>>>>>> >>>>>>> Which leads me to ask: >>>>>>> >>>>>>> 1) Is this error message supposed to be meaningful to me-i.e. a >>>>>>> user-or is >>>>>>> it something that I should be sending to the developer of the >>>>>>> package? >>>>>>> >>>>>>> 2) Is there anything obvious from this that suggests what corrective >>>>>>> action I should be taking? >>>>>>> >>>>>>> >>>>>>> Eric Cabot >>>>>>> University of Wisconsin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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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Eric, You might want to take a look at the getBM function in biomaRt package to see if you can do the conversion. Thanks! Best regards, Julie On 1/5/11 5:31 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: > Julie, > > I don't know how to do that in R. I guess I can always export the > annotations, do the association in Perl and re-import them as a vector to > use with getEnrichedGo. > > Eric > > Zhu, Lihua (Julie) wrote: >> Eric, >> >> You could convert the exon IDs associated with the peaks to ensemble gene >> IDs and input these ensemble gene IDs to the getEnrichedGO function. >> >> Best regards, >> >> Julie >> >> >> On 1/5/11 4:09 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >> >>> Hi Julie, >>> >>> It may be a while before I get back to you on this, because I did my >>> mapping and ChIP-Seq analysis with Hg19 (NCBI 37), not Hg18 (NCBI 36). >>> I'm also a little concerned about using transcription start site >>> annotations rather than exons, because the the binding domains are not >>> thought to be restricted to only promoters. Any suggestions? >>> >>> Eric >>> >>> >>> >>> Zhu, Lihua (Julie) wrote: >>>> Eric, >>>> >>>> The annotated dataset has exon ID instead of gene ID while the >>>> getEnrichedGO >>>> is expecting feature_id_type="ensembl_gene_id". For a list of supported >>>> feature_id_type, please type ?getEnrichedGO. >>>> >>>> To use getEnrichedGO function, first get the TSS annotation. >>>> >>>> TSS.human.NCBI36 = getAnnotation(ENSEMBLE_GENES_MART, featureType="TSS") >>>> >>>> or use the build in TSS as >>>> >>>> data(TSS.human.NCBI36) >>>> >>>> Then annotate your peaks with TSS.human.NCBI36 followed by getEnrichedGO >>>> call. >>>> >>>> Please let me know if this works for you. >>>> >>>> Best regards, >>>> >>>> Julie >>>> >>>> >>>> >>>> >>>> On 1/5/11 12:29 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >>>> >>>>> Hi Julie, >>>>> >>>>> Thank you for your response. >>>>> >>>>> Here is the sessionInfo and traceback output and also a few lines of >>>>> "my_annotated_regions". >>>>> >>>>> Regards, >>>>> >>>>> Eric Cabot >>>>> >>>>>> sessionInfo() >>>>> R version 2.12.1 (2010-12-16) >>>>> 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 >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] ChIPpeakAnno_1.6.0 limma_3.6.9 >>>>> [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 >>>>> [5] RSQLite_0.9-4 DBI_0.2-5 >>>>> [7] AnnotationDbi_1.12.0 >>>>> BSgenome.Ecoli.NCBI.20080805_1.3.16 >>>>> [9] BSgenome_1.18.2 GenomicRanges_1.2.2 >>>>> [11] Biostrings_2.18.2 IRanges_1.8.8 >>>>> [13] multtest_2.6.0 Biobase_2.10.0 >>>>> [15] biomaRt_2.6.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2 >>>>> [5] tools_2.12.1 XML_3.2-0 >>>>> my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs .eg.db",ma >>>>> xP >>>>> =0 >>>>> .01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_id") >>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>>>> argument is of length zero >>>>>> traceback() >>>>> 2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp") >>>>> 1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db", >>>>> maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type = >>>>> "ensembl_gene_id") >>>>> >>>>> >>>>> >>>>>> as.data.frame(my_annotated_regions[1:15,]) >>>>> space start end width names peak strand >>>>> 1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 + >>>>> 2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 + >>>>> 3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 + >>>>> 4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 + >>>>> 5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 + >>>>> 6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 + >>>>> 7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 + >>>>> 8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 + >>>>> 9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 + >>>>> 10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 + >>>>> 11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 + >>>>> 12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 + >>>>> 13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 + >>>>> 14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 + >>>>> 15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 + >>>>> feature start_position end_position insideFeature >>>>> distancetoFeature >>>>> 1 ENSE00001749374 241995237 241996089 downstream >>>>> 2699 >>>>> 2 ENSE00001643382 237144639 237145008 upstream >>>>> -34896 >>>>> 3 ENSE00001807176 236078715 236078821 downstream >>>>> 1552 >>>>> 4 ENSE00001776382 233807017 233807237 downstream >>>>> 46228 >>>>> 5 ENSE00001442190 233749750 233750272 upstream >>>>> -21794 >>>>> 6 ENSE00001731401 230728406 230728586 overlapEnd >>>>> 148 >>>>> 7 ENSE00001439385 229685652 229685769 downstream >>>>> 1477 >>>>> 8 ENSE00001903546 228882063 228882416 downstream >>>>> 61200 >>>>> 9 ENSE00001439386 218303137 218303294 downstream >>>>> 55748 >>>>> 10 ENSE00001624346 212253973 212254092 downstream >>>>> 286 >>>>> 11 ENSE00001903225 210111538 210111622 upstream >>>>> -25274 >>>>> 12 ENSE00001336255 209859550 209859630 downstream >>>>> 3999 >>>>> 13 ENSE00001742112 207438342 207438381 upstream >>>>> -1225 >>>>> 14 ENSE00001782518 190331193 190331400 downstream >>>>> 21207 >>>>> 15 ENSE00001283926 184446520 184446737 upstream >>>>> -13913 >>>>> shortestDistance fromOverlappingOrNearest >>>>> 1 1847 NearestStart >>>>> 2 34637 NearestStart >>>>> 3 1446 NearestStart >>>>> 4 46008 NearestStart >>>>> 5 21646 NearestStart >>>>> 6 32 NearestStart >>>>> 7 1360 NearestStart >>>>> 8 60847 NearestStart >>>>> 9 55591 NearestStart >>>>> 10 167 NearestStart >>>>> 11 25025 NearestStart >>>>> 12 3919 NearestStart >>>>> 13 1078 NearestStart >>>>> 14 21000 NearestStart >>>>> 15 13765 NearestStart >>>>> >>>>> >>>>> Zhu, Lihua (Julie) wrote: >>>>>> Hi Eric, >>>>>> >>>>>> Could you please post the session information with sessionInfo() command? >>>>>> Could you please also send a few ensembl IDs in your annotated dataset? >>>>>> Thanks! >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Julie >>>>>> >>>>>> >>>>>> On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at="" gmail.com=""> wrote: >>>>>> >>>>>>> I am a relatively new Bioconductor user and I am trying to analyze some >>>>>>> ChIP-seq results that came from QuEST using the ChIPpeakAnno package. >>>>>>> >>>>>>> After importing the regions of interest into RangedData objects and >>>>>>> doing >>>>>>> the following: >>>>>>> >>>>>>> >>>>>> ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapien s_gene_ens >>>>>> em >>>>>> bl >>>>>> "> >>>>>> ) >>>>>>> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART, >>>>>>> featureType="ExonPlusUtr") >>>>>>> >>>>>>> >>>>>>> I had no problem annotating and generating a Venn diagram to show the >>>>>>> overlaps between my three sets of peaks. To annotate, I used: >>>>>>> >>>>>>> annotated_regions=annotatePeakInBatch(myranged, >>>>>>> AnnotationData=ENSEMBL_ExonPlus_Annotation) >>>>>>> >>>>>>> >>>>>>> But I cannot seem to get the getEnrichedGo method to work on this (or my >>>>>>> other two annotated regions). Here is a typical command line: >>>>>>> >>>>>>> >>>>>>> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs. eg.db",max >>>>>>> P= >>>>>>> 0. >>>>>>> 01 >>>>>>> ,multiAdj=TRUE,minGOterm=1, >>>>>>> multiAdjMethod="BH",feature_id_type="ensembl_gene_id") >>>>>>> >>>>>>> and here is a typical error message: >>>>>>> >>>>>>> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg. db",maxP=0 >>>>>>> .0 >>>>>>> 1, >>>>>>> mu >>>>>>> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id") >>>>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : >>>>>>> argument is of length zero >>>>>>> >>>>>>> >>>>>>> Which leads me to ask: >>>>>>> >>>>>>> 1) Is this error message supposed to be meaningful to me-i.e. a user-or >>>>>>> is >>>>>>> it something that I should be sending to the developer of the package? >>>>>>> >>>>>>> 2) Is there anything obvious from this that suggests what corrective >>>>>>> action I should be taking? >>>>>>> >>>>>>> >>>>>>> Eric Cabot >>>>>>> University of Wisconsin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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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