[Bioc-devel] Txdb Issues - all exon names are NA's ?
Hervé Pagès
hpages at fredhutch.org
Wed Sep 23 03:03:32 CEST 2015
Hi Marc,
On 09/22/2015 05:39 PM, Marc Carlson wrote:
> Herve is right. UCSC doesn't give us this information, And actually, I
> think it's pretty rare to see exon names from anybody. So it's weird
> to me that they are a default return value for this method.
Ensembl does provide exon names/ids so any TxDb object that was created
with makeTxDbFromBiomart("ensembl", ...) should have them:
library(GenomicFeatures)
txdb <- makeTxDbFromBiomart("ensembl", dataset="celegans_gene_ensembl")
exonsBy(txdb, use.names=TRUE)$Y74C9A.2a.2
# GRanges object with 4 ranges and 3 metadata columns:
# seqnames ranges strand | exon_id exon_name
exon_rank
# <Rle> <IRanges> <Rle> | <integer> <character>
<integer>
# [1] I [10413, 10585] + | 1 WBGene00022276.e1
1
# [2] I [11618, 11689] + | 6 WBGene00022276.e6
2
# [3] I [14951, 15160] + | 11 WBGene00022276.e11
3
# [4] I [16473, 16842] + | 14 WBGene00022276.e14
4
# -------
# seqinfo: 7 sequences (1 circular) from an unspecified genome
Note that the *By() extractors don't let the user choose which column
to return at the moment so that's why it was decided (a long time ago)
to return exon internal ids *and* names (better more than less).
H.
>
> Marc
>
> On Tue, Sep 22, 2015 at 5:29 PM, Hervé Pagès <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
> 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>
>
> $10
> GRanges object with 2 ranges and 2 metadata columns:
> seqnames ranges strand | exon_id exon_name
> [1] chr8 [18248755, 18248855] + | 113603 <NA>
> [2] chr8 [18257508, 18258723] + | 113604 <NA>
>
> ...
> <23457 more elements>
> -------
> seqinfo: 93 sequences (1 circular) from hg19 genome
> > testgr <- unlist(ebg2)
> > table(is.na <http://is.na>(mcols(testgr)$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: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>
> _______________________________________________
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>
>
--
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: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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