Hi Jianhong,
According to my timings, it's a little bit slower than exonsBy() but
not that much. It has to do a little bit more work too as the introns
are not explicitly stored in the SQLite db (the exons are) but are
inferred from the exons and transcript boundaries.
So intronsByTranscript() has to retrieve all the exons + all the
transcripts from the db.
intronsByTranscript():
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
system.time(introns <-
intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene))
# user system elapsed
# 9.165 0.076 9.263
system.time(introns <-
intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene))
# user system elapsed
# 4.824 0.064 4.896
exonsBy():
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
system.time(exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene))
# user system elapsed
# 7.720 0.072 7.812
system.time(exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene))
# user system elapsed
# 4.229 0.028 4.265
transcripts():
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
system.time(tx <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene))
# user system elapsed
# 1.424 0.008 1.436
system.time(tx <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene))
# user system elapsed
# 0.776 0.012 0.790
Less than 10 sec. to retrieve all the exons and transcripts from disk
and compute the 659327 introns. It's actually not that bad.
Cheers,
H.
On 12/20/2013 08:25 AM, Ou, Jianhong wrote:
Dear all,
When I try to use intronsByTranscript to get introns for hg19 known genes, I
found it is unacceptable slow. Does any body has the same problem?
My code:
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
introns <- intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene)
sessionInfo()
R Under development (unstable) (2013-12-12 r64453)
Platform: x86_64-apple-darwin12.5.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.15.4
[3] AnnotationDbi_1.25.9 Biobase_2.23.3
[5] GenomicRanges_1.15.15 XVector_0.3.5
[7] IRanges_1.21.17 BiocGenerics_0.9.2
loaded via a namespace (and not attached):
[1] biomaRt_2.19.1 Biostrings_2.31.5 bitops_1.0-6
BSgenome_1.31.7
[5] DBI_0.2-7 GenomicAlignments_0.99.9 RCurl_1.95-4.1
Rsamtools_1.15.15
[9] RSQLite_0.11.4 rtracklayer_1.23.6 stats4_3.1.0
tools_3.1.0
[13] XML_3.98-1.1 zlibbioc_1.9.0
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
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