because I could get it to work then (see further below).
Anyhow, I'll change the example in derfinder::makeGenomicState and
specify dbType and dbPackage
library('GenomicFeatures')
samplefile <- system.file('extdata', 'UCSC_knownGene_sample.sqlite',
+ package='GenomicFeatures')
old <- loadDb(samplefile)
new <- loadDb(samplefile, dbType = 'TxDb', dbPackage = 'GenomicFeatures')
## For some reason they are not identical.
## My guess is that each one has a different connection, while
everything else is the ## same.
identical(old, new)
[1] FALSE
## However, by 'eye' they look the same
old
TxDb object:
| Db type: TranscriptDb
| Supporting package: GenomicFeatures
| Data source: UCSC
| Genome: hg18
| Genus and Species: Homo sapiens
| UCSC Table: knownGene
| Resource URL: http://genome.ucsc.edu/
| Type of Gene ID: Entrez Gene ID
| Full dataset: no
| miRBase build ID: NA
| transcript_nrow: 135
| exon_nrow: 544
| cds_nrow: 324
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2012-04-13 14:47:54 -0700 (Fri, 13 Apr 2012)
| GenomicFeatures version at creation time: 1.9.4
| RSQLite version at creation time: 0.11.1
| DBSCHEMAVERSION: 1.0
new
TxDb object:
| Db type: TranscriptDb
| Supporting package: GenomicFeatures
| Data source: UCSC
| Genome: hg18
| Genus and Species: Homo sapiens
| UCSC Table: knownGene
| Resource URL: http://genome.ucsc.edu/
| Type of Gene ID: Entrez Gene ID
| Full dataset: no
| miRBase build ID: NA
| transcript_nrow: 135
| exon_nrow: 544
| cds_nrow: 324
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2012-04-13 14:47:54 -0700 (Fri, 13 Apr 2012)
| GenomicFeatures version at creation time: 1.9.4
| RSQLite version at creation time: 0.11.1
| DBSCHEMAVERSION: 1.0
devtools::session_info()
Session
info--------------------------------------------------------------------------
setting value
version R version 3.1.1 (2014-07-10)
system x86_64, darwin10.8.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
Packages------------------------------------------------------------------------------
package * version date source
AnnotationDbi * 1.27.19 2014-10-05 Bioconductor
base64enc 0.1.2 2014-06-26 CRAN (R 3.1.0)
BatchJobs 1.4 2014-09-24 CRAN (R 3.1.1)
BBmisc 1.7 2014-06-21 CRAN (R 3.1.0)
Biobase * 2.25.1 2014-10-09 Bioconductor
BiocGenerics * 0.11.5 2014-09-13 Bioconductor
BiocParallel 0.99.25 2014-10-02 Bioconductor
biomaRt 2.21.5 2014-10-07 Bioconductor
Biostrings 2.33.14 2014-09-09 Bioconductor
bitops 1.0.6 2013-08-17 CRAN (R 3.1.0)
brew 1.0.6 2011-04-13 CRAN (R 3.1.0)
checkmate 1.4 2014-09-03 CRAN (R 3.1.1)
codetools 0.2.9 2014-08-21 CRAN (R 3.1.1)
DBI 0.3.1 2014-09-24 CRAN (R 3.1.1)
devtools 1.6.1 2014-10-07 CRAN (R 3.1.1)
digest 0.6.4 2013-12-03 CRAN (R 3.1.0)
fail 1.2 2013-09-19 CRAN (R 3.1.0)
foreach 1.4.2 2014-04-11 CRAN (R 3.1.0)
futile.logger 1.3.7 2014-01-23 CRAN (R 3.1.0)
futile.options 1.0.0 2010-04-06 CRAN (R 3.1.0)
GenomeInfoDb * 1.1.25 2014-10-02 Bioconductor
GenomicAlignments 1.1.30 2014-09-23 Bioconductor
GenomicFeatures * 1.17.20 2014-10-08 Bioconductor
GenomicRanges * 1.17.47 2014-10-09 Bioconductor
IRanges * 1.99.31 2014-10-07 Bioconductor
iterators 1.0.7 2014-04-11 CRAN (R 3.1.0)
lambda.r 1.1.6 2014-01-23 CRAN (R 3.1.0)
RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1)
Rsamtools 1.17.34 2014-09-20 Bioconductor
RSQLite 0.11.4 2013-05-26 CRAN (R 3.1.0)
rstudioapi 0.1 2014-03-27 CRAN (R 3.1.0)
rtracklayer 1.25.19 2014-10-02 Bioconductor
S4Vectors * 0.2.5 2014-10-08 Bioconductor
sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1)
stringr 0.6.2 2012-12-06 CRAN (R 3.1.0)
XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0)
XVector 0.5.8 2014-09-07 Bioconductor
zlibbioc 1.11.1 2014-04-19 Bioconductor
Cheers,
Leo
