[BioC] Saving/loading Genominator ExpData-class object

rcaloger raffaele.calogero at unito.it
Mon May 24 17:21:02 CEST 2010 

Dear Kasper,
sorry I read the vignette but  missed the point related to the fact that 
ExpData object is essentially just a pointer.
Your example:

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

makes every think clear to me.
Many thanks again.
Raffaele
P.S. Genominator is really a nice piece of software I nicely managed to 
create the table to be used in edgeR in less than an hour  for a project 
of Illumina ncRNA (97 milion mapped reads on 14 samples)  on my portable 
computer.

24/05/2010 15:31, Kasper Daniel Hansen ha scritto:
> 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 rExpData object is essentially just a pointe 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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>>>        
>>      
>    


-- 

----------------------------------------
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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