Question: R session crash with SGSeq::convertToTxFeatures
0
gravatar for oolongoni
2.1 years ago by
oolongoni10
California
oolongoni10 wrote:

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
ADD COMMENTlink modified 2.1 years ago by Leonard Goldstein80 • written 2.1 years ago by oolongoni10
Answer: R session crash with SGSeq::convertToTxFeatures
1
gravatar for Leonard Goldstein
2.1 years ago by
United States
Leonard Goldstein80 wrote:

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          
>
ADD COMMENTlink written 2.1 years ago by Leonard Goldstein80

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"))

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by oolongoni10
Answer: R session crash with SGSeq::convertToTxFeatures
1
gravatar for oolongoni
2.1 years ago by
oolongoni10
California
oolongoni10 wrote:

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

ADD COMMENTlink written 2.1 years ago by oolongoni10
Answer: R session crash with SGSeq::convertToTxFeatures
1
gravatar for Leonard Goldstein
2.1 years ago by
United States
Leonard Goldstein80 wrote:

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

ADD COMMENTlink written 2.1 years ago by Leonard Goldstein80

Thank you! Learned something new!

ADD REPLYlink written 2.1 years ago by oolongoni10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 308 users visited in the last hour