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_na me","mirbase_id","mirbase_accession","external_gene_id"),filters = "ensembl_gene_id", values = feature_ids, mart=mart) > duplicated_ids<-IDs2Add[duplicated(IDs2Add[,"ensembl_gene_id"]),"ens embl_gene_id"] > if(length(duplicated_ids)>0){ > IDs2Add.duplicated<-IDs2Add[IDs2Add[,"ensembl_gene_id"] %in% duplicated_ids,] > IDs2Add.duplicated<-condenseMatrixByColnames(as.matrix(IDs2A dd.duplicated),"ensembl_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 >