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
