[Bioc-devel] very slow to use intronsByTranscript in GenomicFeatures

[James W. MacDonald]

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
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099