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, Herv? Pag?s <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))
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
--
Herv? Pag?s
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>