[Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
Thomas Girke
thomas.girke at ucr.edu
Wed Dec 2 00:50:14 CET 2015
Hi Hervé,
I agree these transcript categories are not very specific, but perhaps
still useful to at least know how many coding/non-coding genes are
represented in a txdb instance coming form UCSC. If it is not much work for
a magician like yourself to support those then it may be worth the effort?
Thomas
On Tue, Dec 1, 2015 at 1:17 PM Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Malcolm,
>
> On 12/01/2015 12:29 PM, Cook, Malcolm wrote:
> >> -----Original Message-----
> > > From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On
> Behalf Of
> > > Hervé Pagès
> > > Sent: Monday, October 26, 2015 12:39 PM
> > > To: Thomas Girke <thomas.girke at ucr.edu>; Arora, Sonali
> > > <sarora at fredhutch.org>; bioc-devel at r-project.org
> > > Subject: Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x,
> exact = exact,
> > > upperBoundIsStrict = !allow.append) :
> > >
> > > Hi Thomas,
> > >
> > > On 10/25/2015 01:06 PM, Thomas Girke wrote:
> > > > I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for
> this error
> > > > was that the tx_type column contains only NA values when a txdb is
> > > generated with
> > > > makeTxDbFromUCSC(). Returning here something more meaningful may be
> > > useful,
> > > > such as the transcript type information available when a txdb is
> generated
> > > > from a GFF.
> > >
> > > We've considered this and might do it at some point. The difficulty
> > > though is that UCSC does not provide this information as part of
> > > the track itself so we'll have to go grab it from some other table
> > > in their huge db through many joins. In the mean time, I'll try to
> > > clarify this in the documentation.
> > >
> >
> > Or, you could pull it from BioMart
>
> That means you need to be able to map UCSC transcripts IDs (uc001aaa.3,
> uc010nxr.1, etc...) to Ensembl transcript IDs (ENST00000456328,
> ENST00000515242, etc...) with the usual complication that only a
> fraction of UCSC IDs are unambiguously mappable. I don't know if that's
> easier/better than grabbing the tx_type directly from UCSC.
>
> OTOH the closest thing to Ensembl transcript_biotype I see in the UCSC
> db is the "category" field in the kgTxInfo table. For example, for hg19,
> the information is here:
>
>
>
> https://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg19&hgta_doSchemaTable=kgTxInfo
>
> It's only one join away from the knownGene table (via the "name"
> column) so should not be too hard to get but it's not as rich as the
> Ensembl transcript_biotype (only 3 possible values at the moment:
> coding, nearCoding, noncoding).
>
> What do people think?
>
> H.
>
> >
> > ~Malcolm
> >
> > > H.
> > >
> > > >
> > > > Thanks,
> > > >
> > > > Thomas
> > > >
> > > > On Fri, Oct 23, 2015 at 12:49:09AM +0000, Thomas Girke wrote:
> > > >> Thanks. Good to know. I have never tried this with an txdb
> instance
> > > >> from makeTxDbFromUCSC(). Will fix this over the weekend.
> > > >> Thomas
> > > >>
> > > >>
> > > >>
> > > >> On Thu, Oct 22, 2015 at 5:39 PM Arora, Sonali <
> sarora at fredhutch.org>
> > > wrote:
> > > >>
> > > >>
> > > >> Hi Thomas,
> > > >>
> > > >> I get the following error when I try to obtain the feature types
> using
> > > >> the function genFeatures()
> > > >>
> > > >>
> > > >>> library(systemPipeR)
> > > >>> library(GenomicFeatures)
> > > >> Loading required package: AnnotationDbi
> > > >>> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
> > > >> Download the refGene table ... OK
> > > >> Download the refLink table ... OK
> > > >> Extract the 'transcripts' data frame ... OK
> > > >> Extract the 'splicings' data frame ... OK
> > > >> Download and preprocess the 'chrominfo' data frame ... OK
> > > >> Prepare the 'metadata' data frame ... OK
> > > >> Make the TxDb object ... OK
> > > >> Warning message:
> > > >> In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :
> > > >> UCSC data anomaly in 359 transcript(s): the cds cumulative length
> is
> > > >> not a multiple of 3 for transcripts 'NM_001037501' 'NM_001277444'
> > > >> 'NM_001037675' 'NM_001271872' 'NM_001170637' 'NM_001300952'
> > > >> 'NM_015326' 'NM_017940' 'NM_001271870' 'NM_001143962'
> > > 'NM_001305275'
> > > >> 'NM_001146344' 'NM_001300891' 'NM_001010890' 'NM_001300891'
> > > >> 'NM_001289974' 'NM_001291281' 'NM_001301371' 'NM_016178'
> > > >> 'NM_001134939' 'NM_001080427' 'NM_001145710' 'NM_001291328'
> > > >> 'NM_001271466' 'NM_001017915' 'NM_005541' 'NM_000348'
> > > 'NM_001145051'
> > > >> 'NM_001135649' 'NM_001128929' 'NM_001080423' 'NM_001144382'
> > > >> 'NM_001291661' 'NM_002958' 'NM_001005861' 'NM_004636'
> > > 'NM_001005914'
> > > >> 'NM_001290060' 'NM_001290061' 'NM_001289930' 'NM_003715'
> > > >> 'NM_001290049' 'NM_001286054' 'NM_001286053' 'NM_001286052'
> > > >> 'NM_182524' 'NM_001075' 'NM_00 [... truncated]
> > > >>> feat <- genFeatures(txdb, featuretype="all", reduce_ranges=TRUE,
> > > >> upstream=1000,
> > > >> + downstream=0, verbose=TRUE)
> > > >> Error in NSBS(i, x, exact = exact, upperBoundIsStrict =
> !allow.append) :
> > > >> subscript contains NAs
> > > >>
> > > >>
> > > >> probably because -
> > > >>
> > > >> Browse[2]> tx
> > > >> GRanges object with 54439 ranges and 3 metadata columns:
> > > >> seqnames ranges strand | tx_name
> > > >> <Rle> <IRanges> <Rle> | <character>
> > > >> [1] chr1 [11874, 14409] + | NR_046018
> > > >> [2] chr1 [30366, 30503] + | NR_036051
> > > >> [3] chr1 [30366, 30503] + | NR_036266
> > > >> [4] chr1 [30366, 30503] + | NR_036267
> > > >> [5] chr1 [30366, 30503] + | NR_036268
> > > >> ... ... ... ... ... ...
> > > >> [54435] chrUn_gl000228 [112605, 114676] + | NM_001306068
> > > >> [54436] chrUn_gl000228 [ 29339, 32226] - | NM_001005217
> > > >> [54437] chrUn_gl000228 [ 29339, 32226] - | NM_001286820
> > > >> [54438] chrUn_gl000241 [ 14739, 36767] - | NR_132315
> > > >> [54439] chrUn_gl000241 [ 16025, 36957] - | NR_132320
> > > >> gene_id tx_type
> > > >> <CharacterList> <character>
> > > >> [1] 100287102 <NA>
> > > >> [2] 100302278 <NA>
> > > >> [3] 100422831 <NA>
> > > >> [4] 100422834 <NA>
> > > >> [5] 100422919 <NA>
> > > >> ... ... ...
> > > >> [54435] 100288687 <NA>
> > > >> [54436] 448831 <NA>
> > > >> [54437] 448831 <NA>
> > > >> [54438] 100289097 <NA>
> > > >> [54439] 102723780 <NA>
> > > >> -------
> > > >> seqinfo: 93 sequences (1 circular) from hg19 genome
> > > >> Browse[2]> unique(mcols(tx)$tx_type)
> > > >> [1] NA
> > > >> debug: tmp <- tx[mcols(tx)$tx_type == tx_type[i]]
> > > >> Browse[2]>
> > > >> Error in NSBS(i, x, exact = exact, upperBoundIsStrict =
> !allow.append) :
> > > >> subscript contains NAs
> > > >>
> > > >>
> > > >> Here is my sessionInfo
> > > >>
> > > >>> sessionInfo()
> > > >> R Under development (unstable) (2015-10-15 r69519)
> > > >> Platform: x86_64-pc-linux-gnu (64-bit)
> > > >> Running under: Ubuntu 14.04.2 LTS
> > > >>
> > > >> 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=en_US.UTF-8 LC_NAME=C
> > > >> [9] LC_ADDRESS=C LC_TELEPHONE=C
> > > >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > > >>
> > > >> attached base packages:
> > > >> [1] parallel stats4 stats graphics grDevices utils datasets
> > > >> [8] methods base
> > > >>
> > > >> other attached packages:
> > > >> [1] GenomicFeatures_1.23.3 AnnotationDbi_1.33.0
> > > >> [3] systemPipeR_1.5.1 RSQLite_1.0.0
> > > >> [5] DBI_0.3.1 ShortRead_1.25.10
> > > >> [7] GenomicAlignments_1.7.1 SummarizedExperiment_1.1.0
> > > >> [9] Biobase_2.31.0 BiocParallel_1.5.0
> > > >> [11] Rsamtools_1.23.0 Biostrings_2.39.0
> > > >> [13] XVector_0.11.0 GenomicRanges_1.21.32
> > > >> [15] GenomeInfoDb_1.7.1 IRanges_2.5.3
> > > >> [17] S4Vectors_0.9.5 BiocGenerics_0.17.0
> > > >>
> > > >> loaded via a namespace (and not attached):
> > > >> [1] Rcpp_0.12.1 lattice_0.20-33 GO.db_3.2.2
> > > >> [4] digest_0.6.8 plyr_1.8.3 futile.options_1.0.0
> > > >> [7] BatchJobs_1.6 ggplot2_1.0.1 zlibbioc_1.17.0
> > > >> [10] annotate_1.49.0 Matrix_1.2-2 checkmate_1.6.2
> > > >> [13] proto_0.3-10 GOstats_2.37.0 splines_3.3.0
> > > >> [16] stringr_1.0.0 pheatmap_1.0.7 RCurl_1.95-4.7
> > > >> [19] biomaRt_2.27.0 munsell_0.4.2 sendmailR_1.2-1
> > > >> [22] rtracklayer_1.31.1 base64enc_0.1-3 BBmisc_1.9
> > > >> [25] fail_1.3 edgeR_3.13.0 XML_3.98-1.3
> > > >> [28] AnnotationForge_1.13.0 MASS_7.3-44 bitops_1.0-6
> > > >> [31] grid_3.3.0 RBGL_1.47.0 xtable_1.7-4
> > > >> [34] GSEABase_1.33.0 gtable_0.1.2 magrittr_1.5
> > > >> [37] scales_0.3.0 graph_1.49.1 stringi_1.0-1
> > > >> [40] hwriter_1.3.2 reshape2_1.4.1 genefilter_1.53.0
> > > >> [43] limma_3.27.0 latticeExtra_0.6-26 futile.logger_1.4.1
> > > >> [46] brew_1.0-6 rjson_0.2.15 lambda.r_1.1.7
> > > >> [49] RColorBrewer_1.1-2 tools_3.3.0 Category_2.37.0
> > > >> [52] survival_2.38-3 colorspace_1.2-6
> > > >>
> > > >>
> > > >>
> > > >>
> > > >> --
> > > >> Thanks and Regards,
> > > >> Sonali
> > > >>
> > > >>
> > > >>
> > > >
> > > > _______________________________________________
> > > > Bioc-devel at 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: hpages at fredhutch.org
> > > Phone: (206) 667-5791
> > > Fax: (206) 667-1319
> > >
> > > _______________________________________________
> > > Bioc-devel at 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: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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