Search
Question: Gviz: UcscTrack function error
0
gravatar for Guest User
5.6 years ago by
Guest User12k
Guest User12k wrote:
I recently upgraded to R 3.0 and BioC 2.12. I upgraded all my BioC packages and having an error with Gviz If I try: chr="chr12" start=57591600 end=57637895 conservation <- UcscTrack(genome = 'mm9', chromosome = chr, track = "Conservation", table = "phyloP30wayPlacental", from = start-2000, to = end+2000, trackType = "DataTrack", start = "start", end = "end", data = "score", type = "hist", window = "auto", col.histogram = "darkblue", fill.histogram = "darkblue", ylim = c(-.5, 4), name = "Conservation") I receive the following error: Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : when 'new2old' is NULL, the first elements in the supplied 'seqlevels' must be identical to 'seqlevels(x)' > traceback() 9: stop("when 'new2old' is NULL, the first elements in the\n", " supplied 'seqlevels' must be identical to 'seqlevels(x)'") 8: makeNewSeqnames(x, new2old = new2old, seqlevels(value)) 7: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) 6: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) 5: normGenomeRange(range, x, single = FALSE) 4: .local(x, ...) 3: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) 2: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) 1: UcscTrack(genome = "mm9", chromosome = chr, track = "Conservation", table = "phyloP30wayPlacental", from = start - 2000, to = end + 2000, trackType = "DataTrack", start = "start", end = "end", data = "score", type = "hist", window = "auto", col.histogram = "darkblue", fill.histogram = "darkblue", ylim = c(-0.5, 4), name = "Conservation") Any suggestions? Thank you, Mike -- output of sessionInfo(): R version 3.0.0 (2013-04-03) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Gviz_1.4.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.22.3 Biobase_2.20.0 BiocGenerics_0.6.0 [4] biomaRt_2.16.0 Biostrings_2.28.0 biovizBase_1.8.0 [7] bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 [10] colorspace_1.2-2 DBI_0.2-6 dichromat_2.0-0 [13] GenomicFeatures_1.12.1 GenomicRanges_1.12.2 Hmisc_3.10-1 [16] IRanges_1.18.0 labeling_0.1 lattice_0.20-15 [19] munsell_0.4 parallel_3.0.0 plyr_1.8 [22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.12.2 [25] RSQLite_0.11.3 rtracklayer_1.20.1 scales_0.2.3 [28] stats4_3.0.0 stringr_0.6.2 tools_3.0.0 [31] XML_3.96-1.1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 5.6 years ago by florian.hahne@novartis.com1.6k • written 5.6 years ago by Guest User12k
0
gravatar for florian.hahne@novartis.com
5.6 years ago by
Switzerland
Hi Michael(s), this looks like a problem in the rtracklayer package. I can reproduce it independently of any of the code in Gviz: session <- browserSession() genome(session) <- "mm9" gr <- GRanges(seqnames="chr12", ranges=IRanges(start=57589600, end=57639895)) ucscTableQuery(session, "cons30way", gr) Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : when 'new2old' is NULL, the first elements in the supplied 'seqlevels' must be identical to 'seqlevels(x)' Would be great if you could take a look, Michael (Lawrence) Florian -- On 5/1/13 6:13 PM, "Michael Morley [guest]" <guest at="" bioconductor.org=""> wrote: > >I recently upgraded to R 3.0 and BioC 2.12. I upgraded all my BioC >packages and having an error with Gviz > >If I try: > >chr="chr12" >start=57591600 >end=57637895 >conservation <- UcscTrack(genome = 'mm9', chromosome = chr, > track = "Conservation", table = >"phyloP30wayPlacental", > from = start-2000, to = end+2000, trackType = >"DataTrack", > start = "start", end = "end", data = "score", > type = "hist", window = "auto", col.histogram = >"darkblue", > fill.histogram = "darkblue", ylim = c(-.5, 4), > name = "Conservation") > > >I receive the following error: > >Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : > when 'new2old' is NULL, the first elements in the > supplied 'seqlevels' must be identical to 'seqlevels(x)' > >> traceback() >9: stop("when 'new2old' is NULL, the first elements in the\n", " >supplied 'seqlevels' must be identical to 'seqlevels(x)'") >8: makeNewSeqnames(x, new2old = new2old, seqlevels(value)) >7: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) >6: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) >5: normGenomeRange(range, x, single = FALSE) >4: .local(x, ...) >3: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) >2: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) >1: UcscTrack(genome = "mm9", chromosome = chr, track = "Conservation", > table = "phyloP30wayPlacental", from = start - 2000, to = end + > 2000, trackType = "DataTrack", start = "start", end = "end", > data = "score", type = "hist", window = "auto", col.histogram = >"darkblue", > fill.histogram = "darkblue", ylim = c(-0.5, 4), name = >"Conservation") > > >Any suggestions? > >Thank you, > >Mike > > > > -- output of sessionInfo(): > >R version 3.0.0 (2013-04-03) >Platform: x86_64-pc-linux-gnu (64-bit) > >locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >attached base packages: >[1] grid stats graphics grDevices utils datasets methods >[8] base > >other attached packages: >[1] Gviz_1.4.1 > >loaded via a namespace (and not attached): > [1] AnnotationDbi_1.22.3 Biobase_2.20.0 BiocGenerics_0.6.0 > [4] biomaRt_2.16.0 Biostrings_2.28.0 biovizBase_1.8.0 > [7] bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 >[10] colorspace_1.2-2 DBI_0.2-6 dichromat_2.0-0 >[13] GenomicFeatures_1.12.1 GenomicRanges_1.12.2 Hmisc_3.10-1 >[16] IRanges_1.18.0 labeling_0.1 lattice_0.20-15 >[19] munsell_0.4 parallel_3.0.0 plyr_1.8 >[22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.12.2 >[25] RSQLite_0.11.3 rtracklayer_1.20.1 scales_0.2.3 >[28] stats4_3.0.0 stringr_0.6.2 tools_3.0.0 >[31] XML_3.96-1.1 zlibbioc_1.6.0 > > >-- >Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 5.6 years ago by florian.hahne@novartis.com1.6k
This took some discussion, but it's finally resolved in devel and release. Michael On Thu, May 2, 2013 at 12:26 AM, Hahne, Florian <florian.hahne@novartis.com>wrote: > Hi Michael(s), > this looks like a problem in the rtracklayer package. I can reproduce it > independently of any of the code in Gviz: > > session <- browserSession() > genome(session) <- "mm9" > gr <- GRanges(seqnames="chr12", ranges=IRanges(start=57589600, > end=57639895)) > ucscTableQuery(session, "cons30way", gr) > Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : > when 'new2old' is NULL, the first elements in the > supplied 'seqlevels' must be identical to 'seqlevels(x)' > > Would be great if you could take a look, Michael (Lawrence) > > Florian > > > > > > -- > > > > > > > On 5/1/13 6:13 PM, "Michael Morley [guest]" <guest@bioconductor.org> > wrote: > > > > >I recently upgraded to R 3.0 and BioC 2.12. I upgraded all my BioC > >packages and having an error with Gviz > > > >If I try: > > > >chr="chr12" > >start=57591600 > >end=57637895 > >conservation <- UcscTrack(genome = 'mm9', chromosome = chr, > > track = "Conservation", table = > >"phyloP30wayPlacental", > > from = start-2000, to = end+2000, trackType = > >"DataTrack", > > start = "start", end = "end", data = "score", > > type = "hist", window = "auto", col.histogram = > >"darkblue", > > fill.histogram = "darkblue", ylim = c(-.5, 4), > > name = "Conservation") > > > > > >I receive the following error: > > > >Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : > > when 'new2old' is NULL, the first elements in the > > supplied 'seqlevels' must be identical to 'seqlevels(x)' > > > >> traceback() > >9: stop("when 'new2old' is NULL, the first elements in the\n", " > >supplied 'seqlevels' must be identical to 'seqlevels(x)'") > >8: makeNewSeqnames(x, new2old = new2old, seqlevels(value)) > >7: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) > >6: `seqinfo<-`(`*tmp*`, value = <s4 object="" of="" class="" "seqinfo"="">) > >5: normGenomeRange(range, x, single = FALSE) > >4: .local(x, ...) > >3: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) > >2: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) > >1: UcscTrack(genome = "mm9", chromosome = chr, track = "Conservation", > > table = "phyloP30wayPlacental", from = start - 2000, to = end + > > 2000, trackType = "DataTrack", start = "start", end = "end", > > data = "score", type = "hist", window = "auto", col.histogram = > >"darkblue", > > fill.histogram = "darkblue", ylim = c(-0.5, 4), name = > >"Conservation") > > > > > >Any suggestions? > > > >Thank you, > > > >Mike > > > > > > > > -- output of sessionInfo(): > > > >R version 3.0.0 (2013-04-03) > >Platform: x86_64-pc-linux-gnu (64-bit) > > > >locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > >attached base packages: > >[1] grid stats graphics grDevices utils datasets methods > >[8] base > > > >other attached packages: > >[1] Gviz_1.4.1 > > > >loaded via a namespace (and not attached): > > [1] AnnotationDbi_1.22.3 Biobase_2.20.0 BiocGenerics_0.6.0 > > [4] biomaRt_2.16.0 Biostrings_2.28.0 biovizBase_1.8.0 > > [7] bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 > >[10] colorspace_1.2-2 DBI_0.2-6 dichromat_2.0-0 > >[13] GenomicFeatures_1.12.1 GenomicRanges_1.12.2 Hmisc_3.10-1 > >[16] IRanges_1.18.0 labeling_0.1 lattice_0.20-15 > >[19] munsell_0.4 parallel_3.0.0 plyr_1.8 > >[22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.12.2 > >[25] RSQLite_0.11.3 rtracklayer_1.20.1 scales_0.2.3 > >[28] stats4_3.0.0 stringr_0.6.2 tools_3.0.0 > >[31] XML_3.96-1.1 zlibbioc_1.6.0 > > > > > >-- > >Sent via the guest posting facility at bioconductor.org. > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by Michael Lawrence10k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 460 users visited in the last hour