forgot to reply to the list...

here's the full output (not including the result of the last timing line,
since that's the offender):

########################################

> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get,
intersect, lapply, Map,
    mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position,
rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'.
To cite Bioconductor,
    see 'citation("Biobase")', and for packages 'citation("pkgname")'.

> TXDB <- TxDb.Hsapiens.UCSC.hg19.knownGene


> sessionInfo()


R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
 LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 GenomicFeatures_1.10.1
[3] AnnotationDbi_1.20.3                    Biobase_2.18.0
[5] GenomicRanges_1.10.5                    IRanges_1.16.4
[7] BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.14.0     Biostrings_2.26.2  bitops_1.0-5
BSgenome_1.26.1    DBI_0.2-5
 [6] parallel_2.15.0    RCurl_1.95-3       Rsamtools_1.10.2
RSQLite_0.11.2     rtracklayer_1.18.1
[11] stats4_2.15.0      tools_2.15.0       XML_3.95-0.1       zlibbioc_1.4.0

########################################


our sessions look pretty much identical, with the exception of R 2.15.0 for
me and 2.15.2 for you.
i'll try to push an upgrade in the next day or so and see if that might
make a difference.

it also occurred to me that the SQLite query can't be the offender, since
this line runs perfectly swiftly:
> foo <- select(TXDB, keys = keys(TXDB), cols = c("TXCHROM", "TXSTRAND",
"TXSTART", "TXEND"), keytype = "GENEID")

so i'm guessing something in the GRangesList construction might be going
haywire?

cheers,

-m


On Tue, Jan 1, 2013 at 5:11 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 01/01/2013 02:05 PM, Martin Morgan wrote:
>
>> On 01/01/2013 01:32 PM, Murat Tasan wrote:
>>
>>> hi all - does anyone have any performance tips for using
>>> transcriptsBy(TXDB, by = "gene") with the UCSC transcript database?
>>> in particular, is the SQLite backing database file indexed (along columns
>>> holding the internal IDs)?
>>> i'd provide some timing results for the command execution, but i ran out
>>> of
>>> patience after about 10 minutes with no results...
>>>
>>
>> it is 'slow' but only in the couple of seconds definition of slow.
>> Something
>> else is going on so a reproducible example, including sessionInfo(),
>> would be
>> helfpul.
>>
>
> Just to follow my own advice...
>
>
>   library(TxDb.Hsapiens.UCSC.**hg19.knownGene)
>   system.time(res <- transcriptsBy(TxDb.Hsapiens.**UCSC.hg19.knownGene,
> by="gene"))
>   length(res)
>   sessionInfo()
>
> gives me
>
> >   library(TxDb.Hsapiens.UCSC.**hg19.knownGene)
> >   system.time(res <- transcriptsBy(TxDb.Hsapiens.**UCSC.hg19.knownGene,
> by="gene"))
>    user  system elapsed
>   3.020   0.012   3.042
> >   length(res)
> [1] 22932
> >   sessionInfo()
> R version 2.15.2 Patched (2012-12-23 r61401)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.**knownGene_2.8.0
> [2] GenomicFeatures_1.10.1
> [3] AnnotationDbi_1.20.3
> [4] Biobase_2.18.0
> [5] GenomicRanges_1.10.5
> [6] IRanges_1.16.4
> [7] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>  [1] biomaRt_2.14.0     Biostrings_2.26.2  bitops_1.0-5
> BSgenome_1.26.1
>  [5] DBI_0.2-5          parallel_2.15.2    RCurl_1.95-3
> Rsamtools_1.10.2
>  [9] RSQLite_0.11.2     rtracklayer_1.18.1 stats4_2.15.2      tools_2.15.2
> [13] XML_3.95-0.1       zlibbioc_1.4.0
>
>
>
>>
>>
>>> cheers,
>>>
>>> -m
>>>
>>>     [[alternative HTML version deleted]]
>>>
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>>> Bioconductor@r-project.org
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>>> http://news.gmane.org/gmane.**science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>
>>>
>>
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
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> Phone: (206) 667-2793
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