Regarding ChIPpeakAnno::getEnrichedGO function
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Aayush, The getEnrichedGO expects annotatedPeak as a RangedData returned from annotatePeakInBatch which contains a field feature, or a character vector containing the feature IDs. Supported feature ID types are ensembl_gene_id, refseq_id, gene_symbol and entrez_id. So for your dataset, you could extract the gene symbols or ensembl IDs. Alternatively, you could change names.ensembl_gene_id to feature. Best regards, Julie On 7/13/11 9:15 PM, "Ayush Raman" <ayush.raman@systemsbiology.org> wrote: Hi Julie, I hope you are doing good. I am trying to do the GO enrichment on a RangedData object. I am running the following command: enrichedGO = getEnrichedGO(m.RangedData, orgAnn="org.Mm.eg.db", maxP= 0.01, multiAdj = TRUE, minGOterm = 10, multiAdjMethod="BH") my m.RangedData object looks like: RangedData with 236 rows and 11 value columns across 202 spaces space ranges | names.ensembl_gene_id names.RefSeqIds names.Entrez.ID <http: names.entrez.id=""> names.Gene.Symbol <character> <iranges> | <character> <factor> <factor> <factor> 1 ENSMUSG00000000489 [ 79826330, 79845238] | ENSMUSG00000000489 NM_011057 18591 Pdgfb 2 ENSMUSG00000000740 [125626250, 125629144] | ENSMUSG00000000740 NM_016738 270106 Rpl13 3 ENSMUSG00000001123 [ 78776476, 78798448] | ENSMUSG00000001123 NM_001159301 16859 Lgals9 4 ENSMUSG00000001123 [ 78776476, 78798448] | ENSMUSG00000001123 NM_010708 16859 Lgals9 5 ENSMUSG00000002699 [ 33946920, 33992295] | ENSMUSG00000002699 NM_010696 16822 Lcp2 6 ENSMUSG00000003135 [ 39591837, 39603726] | ENSMUSG00000003135 NM_028043 52846 D1Bwg0212e 7 ENSMUSG00000003283 [152934204, 152977177] | ENSMUSG00000003283 NM_001172117 15162 Hck 8 ENSMUSG00000003283 [152934204, 152977177] | ENSMUSG00000003283 NM_010407 15162 Hck 9 ENSMUSG00000003437 [ 29177970, 29184407] | ENSMUSG00000003437 NM_019458 54624 Paf1 ... ... ... ... ... ... ... ... 228 ENSMUSG00000074218 [ 30969190, 30971047] | ENSMUSG00000074218 NM_009944 12865 Cox7a1 229 ENSMUSG00000074922 [ 24550992, 24551846] | ENSMUSG00000074922 NM_026520 68034 Fam122a 230 ENSMUSG00000078201 [ 25110959, 25111872] | ENSMUSG00000078201 NM_177344 227615 Tmem203 231 ENSMUSG00000079197 [ 56206278, 56209950] | ENSMUSG00000079197 NM_001029855 19188 Psme2 232 ENSMUSG00000079197 [ 56206278, 56209950] | ENSMUSG00000079197 NM_011190 19188 Psme2 233 ENSMUSG00000079252 [157882856, 157900866] | ENSMUSG00000079252 NM_001160181 240832 Tor1aip2 234 ENSMUSG00000079252 [157882856, 157900866] | ENSMUSG00000079252 NM_022329 240832 Tor1aip2 235 ENSMUSG00000079737 [ 13672022, 13678498] | ENSMUSG00000079737 NM_025653 66598 3110001I22Rik 236 ENSMUSG00000089944 [ 55392211, 55392727] | ENSMUSG00000089944 NM_207635 20088 Rps24 names.OnThreePrimeArray names.DiffExp names.Score names.Other.Gene.Near names.chromosome_name names.start_position <factor> <factor> <factor> <factor> <character> <integer> 1 1 0 10.581459 0 15 79826330 2 0 0 13.226824 0 8 125626250 3 1 1 4.534911 0 11 78776476 4 1 1 4.534911 0 11 78776476 5 1 1 2.645365 0 11 33946920 6 1 0 2.645365 0 1 39591837 7 1 1 2.645365 0 2 152934204 8 1 1 2.645365 0 2 152934204 9 1 0 6.046548 1 7 29177970 ... ... ... ... ... ... ... 228 1 0 3.023274 1 7 30969190 229 1 0 5.668639 1 19 24550992 230 1 0 3.779092 1 2 25110959 231 0 0 2.645365 1 14 56206278 232 0 0 2.645365 1 14 56206278 233 1 1 3.023274 0 1 157882856 234 1 1 3.023274 0 1 157882856 235 1 1 4.91282 1 16 13672022 236 0 0 7.936094 0 1 55392211 names.end_position <integer> 1 79845238 2 125629144 3 78798448 4 78798448 5 33992295 6 39603726 7 152977177 8 152977177 9 29184407 ... ... 228 30971047 229 24551846 230 25111872 231 56209950 232 56209950 233 157900866 234 157900866 235 13678498 236 55392727 Actually I processed bed file and didn't used Annotatedpeak function from ChIPpeakAnno. I performed certain functions got the table as a RangedData object. Now, I am getting a following error after running the getEnrichedGO command: Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : argument is of length zero In addition: Warning message: In is.na <http: is.na=""> (IDs) : is.na <http: is.na=""> () applied to non-(list or vector) of type 'NULL' My session info is as follows: R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RColorBrewer_1.0-2 ChIPpeakAnno_1.6.0 limma_3.6.9 [4] org.Hs.eg.db_2.4.6 GO.db_2.4.5 BSgenome.Ecoli.NCBI.20080805_1.3.16 [7] BSgenome_1.18.3 GenomicRanges_1.2.3 Biostrings_2.18.4 [10] IRanges_1.8.9 multtest_2.7.1 org.Mm.eg.db_2.4.6 [13] RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.12.0 [16] Biobase_2.10.0 biomaRt_2.6.0 loaded via a namespace (and not attached): [1] MASS_7.3-11 RCurl_1.4-3 splines_2.12.0 survival_2.36-5 tools_2.12.0 XML_3.2-0 Please let me know where I am going wrong to correct this error. Any advice/hints will be highly appreciated. Thanks. Aayush Raman Bioinformatics Research Scientist Institute for Systems Biology Seattle WA 206-732-1473 [[alternative HTML version deleted]]
GO ChIPpeakAnno GO ChIPpeakAnno • 744 views
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Ayush Raman ▴ 20
@ayush-raman-4609
Last seen 7.1 years ago
Hi Julie, Thanks a lot. It works now. I appreciate it. Thanks, Aayush Raman Bioinformatics Research Scientist Institute for Systems Biology Seattle WA 206-732-1473 On Thu, Jul 14, 2011 at 6:22 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu>wrote: > Aayush, > > The getEnrichedGO expects annotatedPeak as a RangedData returned from > annotatePeakInBatch which contains a field feature, or a character vector > containing the feature IDs. Supported feature ID types are ensembl_gene_id, > refseq_id, gene_symbol and entrez_id. > > So for your dataset, you could extract the gene symbols or ensembl IDs. > Alternatively, you could change names.ensembl_gene_id to feature. > > Best regards, > > Julie > > > On 7/13/11 9:15 PM, "Ayush Raman" <ayush.raman@systemsbiology.org> wrote: > > Hi Julie, > > I hope you are doing good. I am trying to do the GO enrichment on a > RangedData object. I am running the following command: > > *enrichedGO = getEnrichedGO(m.RangedData, orgAnn="org.Mm.eg.db", maxP= > 0.01, multiAdj = TRUE, minGOterm = 10, multiAdjMethod="BH") > * > my *m.RangedData object* looks like: > > RangedData with 236 rows and 11 value columns across 202 spaces > space ranges | names.ensembl_gene_id > names.RefSeqIds names.Entrez.ID <http: names.entrez.id=""> > names.Gene.Symbol > <character> <iranges> | <character> > <factor> <factor> <factor> > 1 ENSMUSG00000000489 [ 79826330, 79845238] | ENSMUSG00000000489 > NM_011057 18591 Pdgfb > 2 ENSMUSG00000000740 [125626250, 125629144] | ENSMUSG00000000740 > NM_016738 270106 Rpl13 > 3 ENSMUSG00000001123 [ 78776476, 78798448] | ENSMUSG00000001123 > NM_001159301 16859 Lgals9 > 4 ENSMUSG00000001123 [ 78776476, 78798448] | ENSMUSG00000001123 > NM_010708 16859 Lgals9 > 5 ENSMUSG00000002699 [ 33946920, 33992295] | ENSMUSG00000002699 > NM_010696 16822 Lcp2 > 6 ENSMUSG00000003135 [ 39591837, 39603726] | ENSMUSG00000003135 > NM_028043 52846 D1Bwg0212e > 7 ENSMUSG00000003283 [152934204, 152977177] | ENSMUSG00000003283 > NM_001172117 15162 Hck > 8 ENSMUSG00000003283 [152934204, 152977177] | ENSMUSG00000003283 > NM_010407 15162 Hck > 9 ENSMUSG00000003437 [ 29177970, 29184407] | ENSMUSG00000003437 > NM_019458 54624 Paf1 > ... ... ... ... ... > ... ... ... > 228 ENSMUSG00000074218 [ 30969190, 30971047] | ENSMUSG00000074218 > NM_009944 12865 Cox7a1 > 229 ENSMUSG00000074922 [ 24550992, 24551846] | ENSMUSG00000074922 > NM_026520 68034 Fam122a > 230 ENSMUSG00000078201 [ 25110959, 25111872] | ENSMUSG00000078201 > NM_177344 227615 Tmem203 > 231 ENSMUSG00000079197 [ 56206278, 56209950] | ENSMUSG00000079197 > NM_001029855 19188 Psme2 > 232 ENSMUSG00000079197 [ 56206278, 56209950] | ENSMUSG00000079197 > NM_011190 19188 Psme2 > 233 ENSMUSG00000079252 [157882856, 157900866] | ENSMUSG00000079252 > NM_001160181 240832 Tor1aip2 > 234 ENSMUSG00000079252 [157882856, 157900866] | ENSMUSG00000079252 > NM_022329 240832 Tor1aip2 > 235 ENSMUSG00000079737 [ 13672022, 13678498] | ENSMUSG00000079737 > NM_025653 66598 3110001I22Rik > 236 ENSMUSG00000089944 [ 55392211, 55392727] | ENSMUSG00000089944 > NM_207635 20088 Rps24 > names.OnThreePrimeArray names.DiffExp names.Score names.Other.Gene.Near > names.chromosome_name names.start_position > <factor> <factor> <factor> <factor> > <character> <integer> > 1 1 0 10.581459 0 > 15 79826330 > 2 0 0 13.226824 0 > 8 125626250 > 3 1 1 4.534911 0 > 11 78776476 > 4 1 1 4.534911 0 > 11 78776476 > 5 1 1 2.645365 0 > 11 33946920 > 6 1 0 2.645365 0 > 1 39591837 > 7 1 1 2.645365 0 > 2 152934204 > 8 1 1 2.645365 0 > 2 152934204 > 9 1 0 6.046548 1 > 7 29177970 > ... ... ... ... ... > ... ... > 228 1 0 3.023274 1 > 7 30969190 > 229 1 0 5.668639 1 > 19 24550992 > 230 1 0 3.779092 1 > 2 25110959 > 231 0 0 2.645365 1 > 14 56206278 > 232 0 0 2.645365 1 > 14 56206278 > 233 1 1 3.023274 0 > 1 157882856 > 234 1 1 3.023274 0 > 1 157882856 > 235 1 1 4.91282 1 > 16 13672022 > 236 0 0 7.936094 0 > 1 55392211 > names.end_position > <integer> > 1 79845238 > 2 125629144 > 3 78798448 > 4 78798448 > 5 33992295 > 6 39603726 > 7 152977177 > 8 152977177 > 9 29184407 > ... ... > 228 30971047 > 229 24551846 > 230 25111872 > 231 56209950 > 232 56209950 > 233 157900866 > 234 157900866 > 235 13678498 > 236 55392727 > > Actually I processed bed file and didn't used Annotatedpeak function from > ChIPpeakAnno. I performed certain functions got the table as a RangedData > object. > > Now, I am getting a following *error* after running the getEnrichedGO > command: > > *Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { : > argument is of length zero > In addition: Warning message: > In is.na <http: is.na=""> (IDs) : is.na <http: is.na=""> () applied to > non-(list or vector) of type 'NULL' > * > My *session info* is as follows: > > *R version 2.12.0 (2010-10-15) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] RColorBrewer_1.0-2 ChIPpeakAnno_1.6.0 > limma_3.6.9 > [4] org.Hs.eg.db_2.4.6 GO.db_2.4.5 > BSgenome.Ecoli.NCBI.20080805_1.3.16 > [7] BSgenome_1.18.3 GenomicRanges_1.2.3 > Biostrings_2.18.4 > [10] IRanges_1.8.9 multtest_2.7.1 > org.Mm.eg.db_2.4.6 > [13] RSQLite_0.9-4 DBI_0.2-5 > AnnotationDbi_1.12.0 > [16] Biobase_2.10.0 biomaRt_2.6.0 > > > loaded via a namespace (and not attached): > [1] MASS_7.3-11 RCurl_1.4-3 splines_2.12.0 survival_2.36-5 > tools_2.12.0 XML_3.2-0 > * > > > Please let me know where I am going wrong to correct this error. Any > advice/hints will be highly appreciated. > > Thanks. > Aayush Raman > Bioinformatics Research Scientist > Institute for Systems Biology > Seattle WA > 206-732-1473 > > > [[alternative HTML version deleted]]
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