Question: Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
1
Wet&DryImmunology • 220 wrote:
I was learning RNA-seq analysis following the RNA-seq workflow: gene-level exploratory analysis and differential expression.
I came to the step of constructing a TxDb:
gtffile <- file.path(dir,"Homo_sapiens.GRCh37.75_subset.gtf")
> (txdb <- makeTxDbFromGFF(gtffile, format="gtf",circ_seqs=character()))
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning messages:
1: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
2: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
3: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
4: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
Error in dbGetQuery(conn, SQL) :
error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'dbconn' not found
and:
> (ebg <- exonsBy(txdb,by="gene")) Error in exonsBy(txdb, by = "gene") : error in evaluating the argument 'x' in selecting a method for function 'exonsBy': Error: object 'txdb' not found
I guess that I could not ignore the error (and warning?)
Some people also had similar problem with makeTxDbFromGFF
https://support.bioconductor.org/p/70695/
he solved his problem through installing a new version of R and GenomicFeatures, but I don't think that could apply to my problem, for both my R and GenomicFeatures are new:
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.9.5 (Mavericks) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicFeatures_1.20.6 AnnotationDbi_1.30.1 Biobase_2.28.0 [4] Rsamtools_1.20.5 Biostrings_2.36.4 XVector_0.8.0 [7] airway_0.102.0 GenomicRanges_1.20.8 GenomeInfoDb_1.4.3 [10] IRanges_2.4.0 S4Vectors_0.8.0 BiocGenerics_0.14.0 [13] BiocInstaller_1.18.5 loaded via a namespace (and not attached): [1] zlibbioc_1.14.0 GenomicAlignments_1.4.2 BiocParallel_1.2.22 [4] tools_3.2.2 DBI_0.3.1 lambda.r_1.1.7 [7] futile.logger_1.4.1 rtracklayer_1.28.10 futile.options_1.0.0 [10] bitops_1.0-6 RCurl_1.95-4.7 biomaRt_2.24.1 [13] RSQLite_1.0.0 XML_3.98-1.3
Could anyone have any idea how to solve this problem?
Thanks very much!
Sorry I forgot to paste the traceback()
traceback()
13: dbGetQuery(conn, SQL)
12: AnnotationDbi:::dbEasyQuery(AnnotationDbi:::dbconn(annotationdb),
paste(sql, collapse = "\n"))
11: queryAnnotationDb(txdb, sql)
10: load_chrominfo(.self, set.col.class = TRUE)
9: .Object$initialize(...)
8: initialize(value, ...)
7: initialize(value, ...)
6: methods::new(def, ...)
5: .TxDb$new(conn = conn)
4: TxDb(conn)
3: makeTxDb(transcripts, splicings, genes = genes, chrominfo = chrominfo,
metadata = metadata, reassign.ids = TRUE)
2: makeTxDbFromGRanges(gr, metadata = metadata)
1: makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = character())
> (txdb <- makeTxDbFromGFF(gtffile, format="gtf",circ_seqs=character()))
Sorry that if some necessary information is left out, please kindly let me know if any further information is needed to evaluate the problem.
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modified 2.2 years ago
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Biostar ♦♦ 20
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written
4.6 years ago by
Wet&DryImmunology • 220
It looks like GenomicFeatures has some problems, at least on Linux. You have a mix of bioconductor 3.1 (e.g., GenomicFeatures) and 3.2 (e.g., IRanges) packages, which is probably causing the problem.
Yes, actually,that is the problem.
Thank you very much. Ryan.