[BioC] Saving/loading Genominator ExpData-class object

[Kasper Daniel Hansen]

Just to be clear.  In your case you would create the pointer to the
table in the database by

eData <- ExpData(dbFilename = "gilli.db", tablename = "gf11")

Kasper

On Mon, May 24, 2010 at 9:30 AM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> 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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>