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Question: load a TranscriptDb object in another R session?
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gravatar for Sang Chul Choi
5.6 years ago by
Sang Chul Choi230 wrote:
Hi, I made a TranscriptDb object, which worked fine when I use it in the same R session. I want to reuse it by saving the object and loading it in another R session. I got an error like following: > txdb <- makeTranscriptDb (transcripts, splicings, chrominfo=chrominfo) > save(txdb, file="a.rda") ... quit R and rerun R > load("a.rda") > feature.cds <- cds(txdb, columns="exon_name") Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (expired SQLiteConnection) What do I have to reuse a TranscriptDb object in another R session? Thank you, SangChul
ADD COMMENTlink modified 5.6 years ago by Malcolm Cook1.4k • written 5.6 years ago by Sang Chul Choi230
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gravatar for Malcolm Cook
5.6 years ago by
Malcolm Cook1.4k
United States
Malcolm Cook1.4k wrote:
look at the manual for ?saveFeatures ?loadFeatures ~Malcolm > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- > bounces at r-project.org] On Behalf Of Sang Chul Choi > Sent: Friday, April 06, 2012 1:34 PM > To: bioconductor > Subject: [BioC] load a TranscriptDb object in another R session? > > Hi, > > I made a TranscriptDb object, which worked fine when I use it in the same R > session. I want to reuse it by saving the object and loading it in another R > session. I got an error like following: > > > txdb <- makeTranscriptDb (transcripts, splicings, chrominfo=chrominfo) > > save(txdb, file="a.rda") > > ... quit R and rerun R > > > load("a.rda") > > feature.cds <- cds(txdb, columns="exon_name") > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (expired SQLiteConnection) > > What do I have to reuse a TranscriptDb object in another R session? > > Thank you, > > SangChul > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.6 years ago by Malcolm Cook1.4k
The functions you are looking for are: ?saveDb ?loadDb You can also use the older saveFeatures and loadFeatures as Malcolm suggested, but internally, those will now just call the more generically useful functions above. Marc On 04/06/2012 11:51 AM, Cook, Malcolm wrote: > look at the manual for > ?saveFeatures > ?loadFeatures > > > ~Malcolm > > >> -----Original Message----- >> From: bioconductor-bounces at r-project.org [mailto:bioconductor- >> bounces at r-project.org] On Behalf Of Sang Chul Choi >> Sent: Friday, April 06, 2012 1:34 PM >> To: bioconductor >> Subject: [BioC] load a TranscriptDb object in another R session? >> >> Hi, >> >> I made a TranscriptDb object, which worked fine when I use it in the same R >> session. I want to reuse it by saving the object and loading it in another R >> session. I got an error like following: >> >>> txdb<- makeTranscriptDb (transcripts, splicings, chrominfo=chrominfo) >>> save(txdb, file="a.rda") >> ... quit R and rerun R >> >>> load("a.rda") >>> feature.cds<- cds(txdb, columns="exon_name") >> Error in sqliteExecStatement(con, statement, bind.data) : >> RS-DBI driver: (expired SQLiteConnection) >> >> What do I have to reuse a TranscriptDb object in another R session? >> >> Thank you, >> >> SangChul >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 5.6 years ago by Marc Carlson7.2k
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