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

[Thomas Girke]

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.

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
> 
> 
>