[Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

[Thomas Girke]

Hi Hervé and Sonali,
Thanks for looking into this option. Your suggestion makes a lot of sense.
In general, I find it very useful to know what types of transcripts/genes
are included (or missing) in GRanges/GRangesList instances obtained from
txdb objects. For this, the tx_type classification is extremely useful.
Thomas

On Mon, Oct 26, 2015 at 10:38 AM Hervé Pagès <hpages at fredhutch.org> wrote:

> 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.
>
> 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
>

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