[BioC] Saving/loading Genominator ExpData-class object

[Kasper Daniel Hansen]

Hi Raffaele

As described in the user guide: you should not save the ExpData object
as it contains an active connection.

The ExpData object is essentially just a pointer to a table in a
database, so it takes no time to instantiate; hence we see no real
need for saving it.  We might be able to figure out a way to do so,
but we estimated it would take too much time for the little benefit it
would yield.

Kasper

On Mon, May 24, 2010 at 5:58 AM, rcaloger <raffaele.calogero at unito.it> wrote:
> Hi,
> I am loading NGS data in Genominator package.
> Everything is going smoothly in data loading.
>>df <- read.table("s_5_2.ctrl11.txt.25.out.bed", sep="\t", as.is=T)
>>names(df) <- c("chr", "strand", "location")
>>df[1:3,]
>  chr strand  location
> 1   3     -1 121374316
> 2   3     -1 121374316
> 3   3     -1 121374316
>
>>eDataRaw <-  importToExpData(df, "gilli.db", tablename = "gf11")
>> eDataRaw
> table: gf11
> database file: H:\data\gilli\ncRNA\gilli.db
> index columns: chr location strand
> mode: w
> schema:
>      chr  location    strand
> "INTEGER" "INTEGER" "INTEGER"
>
> However, I could not find a specific function to save the Genominator object
> and to load it again.
>  I trayied with save()
> save(eDataRaw,file="eDataRaw.rda")
> but if I load it again I get an error :
>> load("eDataRaw.rda")
>> eDataRaw
> table: gf11
> database file: H:\data\gilli\ncRNA\gilli.db
> index columns: chr location strand
> mode: w
> schema:
> Error in get(.makeDBConnectionName(.Object), .pool) :
>  object "H:\data\gilli\ncRNA\gilli.db___w" non found
> Error in dbGetQuery(con, q) :
>  error in evaluating the argument 'conn' in selecting a method for function
> 'dbGetQuery'
>
> Does anybody know how to save a ExpData-class object?
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
> [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
> [5] LC_TIME=Italian_Italy.1252
>
> attached base packages:
>  [1] grid      tools     tcltk     stats     graphics  grDevices utils
>  [8] datasets  methods   base
>
> other attached packages:
>  [1] Genominator_1.2.0     GenomeGraphs_1.8.0    biomaRt_2.4.0
>  [4] oneChannelGUI_1.15.2  edgeR_1.6.5           IRanges_1.6.0
>  [7] preprocessCore_1.10.0 GOstats_2.14.0        RSQLite_0.8-4
> [10] DBI_0.2-5             graph_1.26.0          Category_2.14.0
> [13] AnnotationDbi_1.10.0  tkWidgets_1.26.0      DynDoc_1.26.0
> [16] widgetTools_1.26.0    affylmGUI_1.22.0      affyio_1.16.0
> [19] affy_1.26.0           limma_3.4.0           Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.26.0   genefilter_1.30.0 GO.db_2.4.1       GSEABase_1.10.0
>  [5] RBGL_1.24.0       RCurl_1.3-1       splines_2.11.0    survival_2.35-8
>  [9] XML_2.8-1         xtable_1.5-6
>>
>
> cheers
> Raffaele
>
> --
>
> ----------------------------------------
> Prof. Raffaele A. Calogero
> Bioinformatics and Genomics Unit
> Dipartimento di Scienze Cliniche e Biologiche
> c/o Az. Ospedaliera S. Luigi
> Regione Gonzole 10, Orbassano
> 10043 Torino
> tel.   ++39 0116705417
> Lab.   ++39 0116705408
> Fax    ++39 0119038639
> Mobile ++39 3333827080
> email: raffaele.calogero at unito.it
>       raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
> Info: http://publicationslist.org/raffaele.calogero
>
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