Hey Marc,
I think your move towards seqlevels is not quite working yet:
samplefile <- system.file("extdata", "UCSC_knownGene_sample.sqlite",
package="GenomicFeatures")
txdb <- loadDb(samplefile)
## This works fine
fiveUTRsByTranscript(txdb)
## This breaks
seqlevels(txdb, force=TRUE) <- "chr6"
fiveUTRsByTranscript(txdb)
Error in relist(x, f) :
shape of 'skeleton' is not compatible with 'NROW(flesh)'
Deep in the guts of this you are trying to build a GRanges object with NAs as
seqlevels, and it doesn't really like that.
Florian
> sessionInfo()
R version 3.0.1 RC (2013-05-12 r62736)
Platform: i386-apple-darwin12.3.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicFeatures_1.13.37 AnnotationDbi_1.23.23 Biobase_2.21.7
[4] GenomicRanges_1.13.43 XVector_0.1.4 IRanges_1.19.36
[7] BiocGenerics_0.7.5 Gviz_1.5.11 BiocInstaller_1.11.4
loaded via a namespace (and not attached):
[1] biomaRt_2.17.2 Biostrings_2.29.18 biovizBase_1.9.2
[4] bitops_1.0-6 BSgenome_1.29.1 cluster_1.14.4
[7] colorspace_1.2-2 DBI_0.2-7 dichromat_2.0-0
[10] Hmisc_3.12-2 labeling_0.2 lattice_0.20-23
[13] munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5
[16] RCurl_1.95-4.1 rpart_4.1-3 Rsamtools_1.13.39
[19] RSQLite_0.11.4 rtracklayer_1.21.11 scales_0.2.3
[22] stats4_3.0.1 stringr_0.6.2 tools_3.0.1
[25] XML_3.98-1.1 zlibbioc_1.7.0
From: Marc Carlson <mcarl...@fhcrc.org<mailto:mcarl...@fhcrc.org>>
Date: Friday, September 13, 2013 7:38 PM
To: Florian Hahne
<florian.ha...@novartis.com<mailto:florian.ha...@novartis.com>>
Cc: "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>"
<bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
Subject: Re: isActiveSeq deprecated
Hi Florian,
Yes we are trying to make things more uniform. seqlevels() lets you rename as
well as deactivate chromosomes you want to ignore, so it was really redundant
with isActiveSeq(). So we are moving away from isActiveSeq() just so that
users have less to learn about. The reason why isActiveSeq was different from
seqlevels was just because it was born for a TranscriptDb (which is based on an
annotation database) instead of being born on a GRanges object. So seqlevels
was the more general tool.
Marc
On 09/13/2013 07:24 AM, Hahne, Florian wrote:
Hi Marc,
I saw these warnings in Gviz, but they stem from GenomicFeatures
Warning messages:
1: 'isActiveSeq' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
2: 'isActiveSeq' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
3: 'isActiveSeq<-' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
4: 'isActiveSeq<-' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
5: 'isActiveSeq' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
6: 'isActiveSeq<-' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
So has the whole idea of active chromosomes in the data base been dropped? I
could not find anything in the change notes. Do I get it right that you can now
do
seqlevels(txdb, force=TRUE) <- "chr1"
if you just want the first chromosome to be active?
Florian
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