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
Thank you! Learned something new!