Hi Sonali, UCSC doesn't provide names for the exons of their gene models. See the table where this data is coming from:
https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=genes&hgta_track=knownGene&hgta_table=knownGene&hgta_doSchema=describe+table+schema The exon information is all coming from the exonStarts and exonEnds columns. No exon names! H. PS: Maybe this would better be asked on the support site. On 09/22/2015 04:44 PM, Arora, Sonali wrote:
Hi everyone, I was trying to get the exons by gene from a txdb object but I get NA's for all exon_name's. Please advise. > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > ebg2 <- exonsBy(txdb, by="gene") > > ebg2 GRangesList object of length 23459: $1 GRanges object with 15 ranges and 2 metadata columns: seqnames ranges strand | exon_id <Rle> <IRanges> <Rle> | <integer> [1] chr19 [58858172, 58858395] - | 250809 [2] chr19 [58858719, 58859006] - | 250810 [3] chr19 [58859832, 58860494] - | 250811 [4] chr19 [58860934, 58862017] - | 250812 [5] chr19 [58861736, 58862017] - | 250813 ... ... ... ... ... ... [11] chr19 [58868951, 58869015] - | 250821 [12] chr19 [58869318, 58869652] - | 250822 [13] chr19 [58869855, 58869951] - | 250823 [14] chr19 [58870563, 58870689] - | 250824 [15] chr19 [58874043, 58874214] - | 250825 exon_name <character> [1] <NA> [2] <NA> [3] <NA> [4] <NA> [5] <NA> ... ... [11] <NA> [12] <NA> [13] <NA> [14] <NA> [15] <NA> $10 GRanges object with 2 ranges and 2 metadata columns: seqnames ranges strand | exon_id exon_name [1] chr8 [18248755, 18248855] + | 113603 <NA> [2] chr8 [18257508, 18258723] + | 113604 <NA> ... <23457 more elements> ------- seqinfo: 93 sequences (1 circular) from hg19 genome > testgr <- unlist(ebg2) > table(is.na(mcols(testgr)$exon_name)) TRUE 272776 > sessionInfo() R version 3.2.2 RC (2015-08-09 r68965) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats4 parallel stats graphics grDevices utils [7] datasets methods base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.1 [2] GenomicFeatures_1.21.29 [3] AnnotationDbi_1.31.18 [4] Biobase_2.29.1 [5] GenomicRanges_1.21.28 [6] GenomeInfoDb_1.5.16 [7] IRanges_2.3.21 [8] S4Vectors_0.7.18 [9] BiocGenerics_0.15.6 loaded via a namespace (and not attached): [1] XVector_0.9.4 zlibbioc_1.15.0 [3] GenomicAlignments_1.5.17 BiocParallel_1.3.52 [5] tools_3.2.2 SummarizedExperiment_0.3.9 [7] DBI_0.3.1 lambda.r_1.1.7 [9] futile.logger_1.4.1 rtracklayer_1.29.27 [11] futile.options_1.0.0 bitops_1.0-6 [13] RCurl_1.95-4.7 biomaRt_2.25.3 [15] RSQLite_1.0.0 Biostrings_2.37.8 [17] Rsamtools_1.21.17 XML_3.98-1.3
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel