Depends on what you mean by unacceptably slow. Took me almost 20
seconds, during which time I got pretty fidgety.
> system.time(introns <-
intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene))
user system elapsed
18.741 0.204 19.340
How long did it take you, and how much RAM do you have?
Best,
Jim
On 12/20/2013 11:25 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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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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