[BioC] Saving/loading Genominator ExpData-class object

[rcaloger]

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