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 <sar...@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 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel