Paolo, Just to let you know that starting with ChIPpeakAnno 2.5.11, you can pass a mart object to addGeneIDs instead of orgAnn. Thanks for your input! Best regards, Julie On 7/30/12 4:51 AM, "Paolo Kunderfranco" <paolo.kunderfranco at="" gmail.com=""> wrote: > Hello, > Ok perfect now is working fine, > Thanks again for your precious help, > Paolo > > > 2012/7/27 Ou, Jianhong <jianhong.ou at="" umassmed.edu="">: >> Hi Paolo, >> >> Because the org database do not contain the info for ENSMUSG00000089245, >> there will show an error by addGeneIDs. >> In this case, you'd better use biomaRt to get the annotation, please try, >> >> feature_ids <- unique(annotatedPeak$feature) >> feature_ids<-feature_ids[!is.na(feature_ids)] >> feature_ids<-feature_ids[feature_ids!=""] >> mart<-useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") >> IDs2Add<-getBM(attributes=c("ensembl_gene_id","mirbase_transcript_n ame","mirb >> ase_id","mirbase_accession","external_gene_id"),filters = "ensembl_gene_id", >> values = feature_ids, mart=mart) >> duplicated_ids<-IDs2Add[duplicated(IDs2Add[,"ensembl_gene_id"]),"en sembl_gene >> _id"] >> if(length(duplicated_ids)>0){ >> IDs2Add.duplicated<-IDs2Add[IDs2Add[,"ensembl_gene_id"] %in% >> duplicated_ids,] >> >> IDs2Add.duplicated<-condenseMatrixByColnames(as.matrix(IDs2Add.dupl icated),"e >> nsembl_gene_id") >> IDs2Add<-IDs2Add[!(IDs2Add[,"ensembl_gene_id"] %in% duplicated_ids),] >> IDs2Add<-rbind(IDs2Add,IDs2Add.duplicated) >> } >> >> And then merge the useful information to the annotatedPeak. >> >> If you have any questions, please let me know. >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu >> >> >> On Jul 27, 2012, at 9:57 AM, Zhu, Lihua (Julie) wrote: >> >>> Paolo, >>> >>> Could you please send us a few rows of miRNAs in annotatedPeaks? Thanks! >>> >>> Best regards, >>> >>> Julie >>> ________________________________________ >>> From: bioconductor-bounces at r-project.org >>> [bioconductor-bounces at r-project.org] on behalf of Paolo Kunderfranco >>> [paolo.kunderfranco at gmail.com] >>> Sent: Friday, July 27, 2012 5:50 AM >>> To: bioconductor at r-project.org >>> Subject: [BioC] ChIPpeakAnno to find peaks nearest to miRNA >>> >>> Dear All, >>> I would like to use ChIPpeakAnno to find peaks nearest to miRNA. >>> >>> I loaded my bed file and created a ranged data, load >>> mmusculus_gene_ensembl dataset through mart and annotated my peaks, >>> and it seems ok, >>> >>> test.rangedData = BED2RangedData(test.bed) >>> mart<-useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") >>> Annotation = getAnnotation(mart, featureType="miRNA") >>> annotatedPeak = annotatePeakInBatch(test.rangedData, >>> AnnotationData=Annotation) >>> as.data.frame(annotatedPeak) >>> >>> <factor> <iranges> | <character> <character> >>> <character> <numeric> <numeric> <character> >>> MACS_peak_109 ENSMUSG00000089245 1 [54494876, 54496209] | >>> MACS_peak_109 + ENSMUSG00000089245 54826062 >>> 54826166 upstream >>> numeric> <numeric> <character> >>> -331186 329853 NearestStart >>> >>> >>> Now I would like to add miRNA Id as I already did when I annotated for >>> TSS, but something goes wrong, any ideas how to solve it? >>> >>> library("org.Mm.eg.db") >>> b<- addGeneIDs(annotatedPeak,"org.Mm.eg.db",c("symbol")) >>> Error: No entrez identifier can be mapped by input data based on the >>> feature_id_type. Please consider to use correct feature_id_type, >>> orgAnn or annotatedPeak >>> >>> >>> Thanks, >>> >>> Paolo >>> >>> >>>> traceback() >>> 2: stop("No entrez identifier can be mapped by input data based on the >>> feature_id_type.\nPlease consider to use correct feature_id_type, >>> orgAnn or annotatedPeak\n", >>> call. = FALSE) >>> 1: addGeneIDs(annotatedPeak, "org.Mm.eg.db", c("symbol")) >>>> sessionInfo() >>> R version 2.15.0 (2012-03-30) >>> Platform: i386-pc-mingw32/i386 (32-bit) >>> >>> locale: >>> [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 >>> LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C >>> [5] LC_TIME=Italian_Italy.1252 >>> >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] targetscan.Mm.eg.db_0.5.0 BiocInstaller_1.4.7 >>> org.Mm.eg.db_2.7.1 ChIPpeakAnno_2.4.0 >>> [5] limma_3.12.1 org.Hs.eg.db_2.7.1 >>> GO.db_2.7.1 RSQLite_0.11.1 >>> [9] DBI_0.2-5 AnnotationDbi_1.18.1 >>> BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.24.0 >>> [13] GenomicRanges_1.8.7 Biostrings_2.24.1 >>> IRanges_1.14.4 multtest_2.12.0 >>> [17] Biobase_2.16.0 biomaRt_2.12.0 >>> BiocGenerics_0.2.0 gplots_2.11.0 >>> [21] MASS_7.3-19 KernSmooth_2.23-8 >>> caTools_1.13 bitops_1.0-4.1 >>> [25] gdata_2.11.0 gtools_2.7.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.91-1.1 splines_2.15.0 stats4_2.15.0 >>> survival_2.36-14 tools_2.15.0 XML_3.9-4.1 >>> >>> _______________________________________________ >>> 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 >>