R session crash with SGSeq::convertToTxFeatures
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oolongoni ▴ 10
@oolongoni-2289
Last seen 3.8 years ago
California

R session on macOS Sierra crashes when making a TxFeatures class from TxDb

library(SGSeq)

## make a TxDb object
hsaEnsembl <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl")
## make a TxFeatures class
txf <- convertToTxFeatures(hsaEnsembl)

R behaves fine when using the TxDb downloaded from BioConductor

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

I've done all my RNA-Seq mapping by STAR using Ensembl annotations. Is this the best way to get TxFeatures object with Ensembl exon names?

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 GenomicFeatures_1.28.5                  AnnotationDbi_1.38.2                    Biobase_2.36.2                         
[5] GenomicRanges_1.28.5                    GenomeInfoDb_1.12.2                     IRanges_2.10.3                          S4Vectors_0.14.4                       
[9] BiocGenerics_0.22.0                    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               XVector_0.16.0             GenomicAlignments_1.12.2   zlibbioc_1.22.0            BiocParallel_1.10.1        bit_1.1-12                 lattice_0.20-35           
 [8] rlang_0.1.2                blob_1.1.0                 tools_3.4.1                grid_3.4.1                 SummarizedExperiment_1.6.4 DBI_0.7                    matrixStats_0.52.2        
[15] bit64_0.9-7                digest_0.6.12              tibble_1.3.4               Matrix_1.2-11              GenomeInfoDbData_0.99.0    rtracklayer_1.36.4         bitops_1.0-6              
[22] RCurl_1.95-4.8             biomaRt_2.32.1             memoise_1.1.0              RSQLite_2.0                DelayedArray_0.2.7         compiler_3.4.1             Rsamtools_1.28.0          
[29] Biostrings_2.44.2          XML_3.98-1.9               pkgconfig_2.0.1
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures • 738 views
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@leonard-goldstein-6845
Last seen 11 months ago
United States

I could run this without any issues. If the problem persists maybe you can try reinstalling R and Bioconductor? 

> library(GenomicFeatures)
> library(SGSeq)
> hsaEnsembl <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl")
> txf <- convertToTxFeatures(hsaEnsembl)
> 
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SGSeq_1.10.0               SummarizedExperiment_1.6.4 DelayedArray_0.2.7         matrixStats_0.52.2         Rsamtools_1.28.0          
 [6] Biostrings_2.44.2          XVector_0.16.0             GenomicFeatures_1.28.5     AnnotationDbi_1.38.2       Biobase_2.36.2            
[11] GenomicRanges_1.28.5       GenomeInfoDb_1.12.2        IRanges_2.10.3             S4Vectors_0.14.4           BiocGenerics_0.22.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12             compiler_3.4.1           bitops_1.0-6             tools_3.4.1              zlibbioc_1.22.0         
 [6] biomaRt_2.32.1           digest_0.6.12            bit_1.1-12               RSQLite_2.0              memoise_1.1.0           
[11] tibble_1.3.4             lattice_0.20-35          pkgconfig_2.0.1          rlang_0.1.2              Matrix_1.2-11           
[16] igraph_1.1.2             DBI_0.7                  GenomeInfoDbData_0.99.0  rtracklayer_1.36.4       bit64_0.9-7             
[21] grid_3.4.1               XML_3.98-1.9             BiocParallel_1.10.1      magrittr_1.5             blob_1.1.0              
[26] GenomicAlignments_1.12.2 RUnit_0.4.31             RCurl_1.95-4.8          
>
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0
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I decided to raze everything (~/.Rhistory; ~/.Rapp.history, ~/Library/R/3.x/, etc) and then re-installed R and the libraries. Now everything works!

> install.packages("RSQLite")

> source("https://bioconductor.org/biocLite.R")

> biocLite(c("GenomicFeatures", "AnnotationDbi", "SGSeq"))

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oolongoni ▴ 10
@oolongoni-2289
Last seen 3.8 years ago
California

I uninstalled R and RStudio, then re-installed both. The crash persists. Is there a workaround using other TxDb but annotated by ENSEMBL notations?

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@leonard-goldstein-6845
Last seen 11 months ago
United States

Hi, since I can't reproduce the problem it is difficult to troubleshoot. As an alternative to TxDb objects, the convertToTxFeatures function also accepts a GRangesList of exons grouped by transcript. So you could try something like this

> tx <- exonsBy(hsaEnsembl, "tx", use.names = TRUE)
> mcols(tx)$txName <- names(tx)
> df <- select(hsaEnsembl, names(tx), "GENEID", "TXNAME")
> mcols(tx)$geneName <- df$GENEID[match(names(tx), df$TXNAME)]
> txf <- convertToTxFeatures(tx)

Leonard

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Thank you! Learned something new!

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