Re: [Bioc-devel] isActiveSeq deprecated
Same view here, with all the different data types that are around in the Bioconductor world these days it seems to me that a consistent behaviour is preferable. Florian On 9/24/13 8:22 AM, Hervé Pagès hpa...@fhcrc.org wrote: Hi Florian, Marc, On 09/18/2013 11:55 PM, Hahne, Florian wrote: Hi Marc, Herve, I also noticed this behaviour: library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb - TxDb.Hsapiens.UCSC.hg19.knownGene seqlevels(txdb, force=TRUE) - c(chr1, ch2) oldLevs - seqlevels(txdb) seqlevels(txdb, force=TRUE) - chr1 seqlevels(txdb, force=TRUE) - oldLevs Error in .seqinfo.TranscriptDbReplace(x, new2old = new2old, force = force, : The replacement value must be either a 1 to 1 replacement or a subset of the original set when replacing the 'seqinfo' of a TranscriptDb object But: restoreSeqlevels(txdb) seqlevels(txdb, force=TRUE) - oldLevs This is probably intentional, but I found it to be rather confusing. If one should be able to use the seqlevels replacement method to control active and inactive chromosomes in the TranscriptDb object, then having this mandatory step of restoring all chromosomes to the active state followed by another restriction to be quite cumbersome. At least a somewhat more useful error message would help in that case. Or couldn't the replacement method always call restoreSeqlevels internally. Somewhat related to this, I also found the following issue: library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb - TxDb.Hsapiens.UCSC.hg19.knownGene seqlevels(txdb, force=TRUE) - chrM seqlengths(txdb) chrM 16571 seqlevels(txdb) - chr1 seqlengths(txdb) chr1 16571 The 2nd call to the seqlevels() setter actually performed a *renaming* operation (a clue for this is that I didn't have to use force=TRUE). Renaming the seqlevels of a TranscriptDb object is something I think we want to support, e.g. when there is the need to use a different naming convention (like in seqlevels(txdb) - M). This is exactly the syntax that one would use to rename the seqlevels of a GRanges object: gr - GRanges(chrM, IRanges(1:2, 10)) seqlevels(gr) - chr1 gr GRanges with 2 ranges and 0 metadata columns: seqnamesranges strand Rle IRanges Rle [1] chr1 [1, 10] * [2] chr1 [2, 10] * --- seqlengths: chr1 NA There is nothing that prevents the user from doing this kind of silly renaming except that, in the case of the TranscriptDb object, this is almost certainly not what the user intended to do. What s/he really wanted was selecting chr1 instead of chrM, which can be achieved with: restoreSeqlevels(txdb) seqlevels(txdb, force=TRUE) - chr1 seqlengths(txdb) chr1 249250621 Yes having to restore all chromosomes to the active state before one can make a new selection is cumbersome so we probably need to revisit this. It would also help to point out somewhere (I may have missed it) that TranscriptDb seqlevels (or rather the internal GRanges) are actually pass by reference: txdb2 - txdb seqlevels(txdb) seqlevels(txdb2) restoreSeqlevels(txdb) seqlevels(txdb2) That's because TranscriptDb is a reference class. IMHO it shouldn't. Also Herve: what is the definition of a used seqlevel? Does that mean that a factor level is defined, but no range in the GRanges object is assigned this level? Yes. Like here: gr - GRanges(chrM, IRanges(1:2, 10), seqlengths=c(chr1=5000, chrM=25)) gr GRanges with 2 ranges and 0 metadata columns: seqnamesranges strand Rle IRanges Rle [1] chrM [1, 10] * [2] chrM [2, 10] * --- seqlengths: chr1 chrM 5000 25 Only chrM is in use: seqlevelsInUse(gr) [1] chrM The idiom to drop seqlevels that are not in use is: seqlevels(gr) - seqlevelsInUse(gr) gr GRanges with 2 ranges and 0 metadata columns: seqnamesranges strand Rle IRanges Rle [1] chrM [1, 10] * [2] chrM [2, 10] * --- seqlengths: chrM 25 Of course, in that case, force=TRUE is not needed because the operation is guaranteed to not shrink the GRanges object. Why would those exists in a TranscriptDb object at all? The notion of seqlevels in use is not formally defined for a TranscriptDb object: seqlevelsInUse(txdb) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ŒseqlevelsInUse¹ for signature ŒTranscriptDb¹ but it could be: a seqlevel or chromosome could be considered to be in use if there is at least 1 feature (transcript, exon or CDS) in the db that is on it. I think for most TranscriptDb objects, all the seqlevels are actually in use. However it's conceivable that a TranscriptDb object could have some extra seqlevels that are not in use (the seqlevels + their lengths + their circularity flags are
Re: [Bioc-devel] isActiveSeq deprecated
Hi Marc, Wouldn't it make sense to just ignore the 'force' arg when dropping the seqlevels of a TranscriptDb? The 'force' argument is FALSE by default and this prevents seqlevels- to shrink GRanges or other vector-like objects when the user tries to drop seqlevels that are in use. Internally seqlevels- calls seqlevelsInUse() to get the seqlevels currently in use and see if they intersect with the seqlevels to drop. In the TranscriptDb situation, people always have to use 'force=TRUE' to drop seqlevels, regardless of whether the levels to drop are in use or not (the seqlevelsInUse() getter not being defined for TranscriptDb objects, I suspect seqlevels- doesn't look at this). So maybe 'force' could just be ignored for TranscriptDb objects? That would make seqlevels- a little bit more user-friendly on those objects. Thanks, H. On 09/13/2013 10:38 AM, Marc Carlson wrote: 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] isActiveSeq deprecated
I actually considered this, but I opted to do it this way just for the sake of being consistent (which was my whole mission for implementing seqlevels in here in the 1st place). Now I could make it more convenient here and break consistency with how it is used elsewhere, but what do people prefer? Consistent or convenient? Marc On 09/18/2013 10:40 AM, Hervé Pagès wrote: Hi Marc, Wouldn't it make sense to just ignore the 'force' arg when dropping the seqlevels of a TranscriptDb? The 'force' argument is FALSE by default and this prevents seqlevels- to shrink GRanges or other vector-like objects when the user tries to drop seqlevels that are in use. Internally seqlevels- calls seqlevelsInUse() to get the seqlevels currently in use and see if they intersect with the seqlevels to drop. In the TranscriptDb situation, people always have to use 'force=TRUE' to drop seqlevels, regardless of whether the levels to drop are in use or not (the seqlevelsInUse() getter not being defined for TranscriptDb objects, I suspect seqlevels- doesn't look at this). So maybe 'force' could just be ignored for TranscriptDb objects? That would make seqlevels- a little bit more user-friendly on those objects. Thanks, H. On 09/13/2013 10:38 AM, Marc Carlson wrote: 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] isActiveSeq deprecated
Note that currently it's kind of inconsistent anyway because it doesn't look at the seqlevels that are in use. For example: library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb - TxDb.Hsapiens.UCSC.hg19.knownGene Trying to drop chrUn_gl000249 (which I know is not in use): seqlevels(txdb) - setdiff(seqlevels(txdb), chrUn_gl000249) Error in .seqinfo.TranscriptDbReplace(x, new2old = new2old, force = force, : You need to use force=TRUE if you want to drop seqlevels. 'force=TRUE' should only be required when trying to drop seqlevels that are in use. So the choice are more between: (a) consistent, (b) convenient, or (c) leave it as it is (which is neither convenient or consistent). I vote for (b). H. On 09/18/2013 11:31 AM, Marc Carlson wrote: I actually considered this, but I opted to do it this way just for the sake of being consistent (which was my whole mission for implementing seqlevels in here in the 1st place). Now I could make it more convenient here and break consistency with how it is used elsewhere, but what do people prefer? Consistent or convenient? Marc On 09/18/2013 10:40 AM, Hervé Pagès wrote: Hi Marc, Wouldn't it make sense to just ignore the 'force' arg when dropping the seqlevels of a TranscriptDb? The 'force' argument is FALSE by default and this prevents seqlevels- to shrink GRanges or other vector-like objects when the user tries to drop seqlevels that are in use. Internally seqlevels- calls seqlevelsInUse() to get the seqlevels currently in use and see if they intersect with the seqlevels to drop. In the TranscriptDb situation, people always have to use 'force=TRUE' to drop seqlevels, regardless of whether the levels to drop are in use or not (the seqlevelsInUse() getter not being defined for TranscriptDb objects, I suspect seqlevels- doesn't look at this). So maybe 'force' could just be ignored for TranscriptDb objects? That would make seqlevels- a little bit more user-friendly on those objects. Thanks, H. On 09/13/2013 10:38 AM, Marc Carlson wrote: 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] isActiveSeq deprecated
Makes sense. Thanks. I'll update my code. Florian From: Marc Carlson mcarl...@fhcrc.orgmailto:mcarl...@fhcrc.org Date: Friday, September 13, 2013 7:38 PM To: Florian Hahne florian.ha...@novartis.commailto:florian.ha...@novartis.com Cc: bioc-devel@r-project.orgmailto:bioc-devel@r-project.org bioc-devel@r-project.orgmailto: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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] isActiveSeq deprecated
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_1.0-6BSgenome_1.29.1 cluster_1.14.4 [7] colorspace_1.2-2DBI_0.2-7 dichromat_2.0-0 [10] Hmisc_3.12-2labeling_0.2lattice_0.20-23 [13] munsell_0.4.2 plyr_1.8RColorBrewer_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_3.0.1stringr_0.6.2 tools_3.0.1 [25] XML_3.98-1.1zlibbioc_1.7.0 From: Marc Carlson mcarl...@fhcrc.orgmailto:mcarl...@fhcrc.org Date: Friday, September 13, 2013 7:38 PM To: Florian Hahne florian.ha...@novartis.commailto:florian.ha...@novartis.com Cc: bioc-devel@r-project.orgmailto:bioc-devel@r-project.org bioc-devel@r-project.orgmailto: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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] isActiveSeq deprecated
Thanks Florian, I just checked in a fix for this. Please let me know if you find any other quirks. Marc On 09/16/2013 05:33 AM, Hahne, Florian wrote: 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_1.0-6BSgenome_1.29.1 cluster_1.14.4 [7] colorspace_1.2-2DBI_0.2-7 dichromat_2.0-0 [10] Hmisc_3.12-2labeling_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_3.0.1stringr_0.6.2 tools_3.0.1 [25] XML_3.98-1.1zlibbioc_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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] isActiveSeq deprecated
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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
