Galaxy -> cummeRbund How?

[ekimmike]

Hi,

I process my data using Galaxy due to the lack of good server, everything work fine Tophat->Cufflink->Cuffcompare->Cuffdiff (these files look fine)

Problem starts when try to open them from R and I cannot force cummeRbund to load the files to db that I import from Galaxy, should I combine them somehow, or simply place in one directory.

I would really appreciate your help.

Best!

[ekimmike]

some more details...

> cuff<-readCufflinks("~XXX/RNAseq/proteinA")
Creating database ~XXX/RNAseq/proteinA/cuffData.db
Reading ~~XXX/RNAseq/proteinA/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (unable to bind data for parameter ':status')
In addition: Warning messages:
1: In `[<-.factor`(`*tmp*`, ri, value = c(0, 127890, 493903, 358.358, :
invalid factor level, NAs generated
2: In `[<-.factor`(`*tmp*`, ri, value = c(0, 127470, 481005, 262.821, :
invalid factor level, NAs generated
3: In `[<-.factor`(`*tmp*`, ri, value = c(0, 128310, 506801, 453.896, :
invalid factor level, NAs generated
4: In `[<-.factor`(`*tmp*`, ri, value = c(0, 886.049, 8123.86, 2.0214, :
invalid factor level, NAs generated
5: In `[<-.factor`(`*tmp*`, ri, value = c(0, 619.614, 0, 0, 11.9375, :
invalid factor level, NAs generated
6: In `[<-.factor`(`*tmp*`, ri, value = c(0, 1152.48, 4298850, 4.56339, :
invalid factor level, NAs generated

[Carlos Borroto]

Hi,

If you only tell readCufflinks the directory with the files from Galaxy, you will need to first make sure you rename all the files to the default names cuffdiff usually uses. My recommendation would be to instead specify each argument manually.

Something like this

 
cuff <- readCufflinks(dir = "path/to/galaxy/output/",
                         dbFile = "output_database",
                         geneFPKM = "genes_fpkm_tracking",
                         geneDiff = "genes_exp",
                         isoformFPKM = "isoforms_fpkm_tracking",
                         isoformDiff = "isoforms_exp",
                         TSSFPKM = "tss_groups_fpkm_tracking",
                         TSSDiff = "tss_groups_exp",
                         CDSFPKM = "cds_fpkm_tracking",
                         CDSExpDiff = "cds_exp_diff",
                         CDSDiff = "cds_diff",
                         promoterFile = "promoters_diff",
                         splicingFile = "splicing_diff",
                         rebuild = T)

Hope it helps,
Carlos

[saran.ela123]

hi,

Doubt clarification.

what is that output_database ?

[IBseq]

hi all,
can anyone tell em how to fix this?

head(features(myGene))
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "features", for signature "CuffGene"


thanks,
ibseq

[EdRyder]

Just found this thread as I had the same problem as above for:
...
head(features(myGene))
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "features", for signature "CuffGene"
...
and managed to find the cause

The problem is if you load the library("GenomicFeatures") explicitly, to make a txdb object for example, it somehow stops the features(myGene) from working. The trick is to load CummeRbund, load GenomicFeatures, do what you need with the latter, then unload GenomicFeatures again. It will complain that it can't, but seems to fix the issue nonetheless.

Using R 3.6.0 and BioConductor 3.9, in windows and CentOS Linux.

--Ed