proActiv throws an error if input file is a xz-compressed TopHat2 junction BED file (.bed.xz). This behaviour stems from readTopHatJunctions (GenomicAlignments package).
> readTopHatJunctions('../sample1.bed.xz')
Error in validObject(.Object) :
invalid class “BEDFile” object: invalid object for slot "resource" in class "BEDFile": got class "xzfile", should be or extend class "characterORconnection"
In addition: Warning message:
In readTopHatJunctions("../junction-files/sample3.bed.xz") :
'file' has no .bed extension, suggesting it may not be a junctions.bed
file as generated by TopHat. I will assume it is this file anyway (or a BED
file with similar content). If 'file' is a tab-delimited file obtained
by running TopHat's bed_to_juncs script on a junctions.bed file, you
should use 'file.is.raw.juncs=TRUE'
Session info:
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_Singapore.1252 LC_CTYPE=English_Singapore.1252 LC_MONETARY=English_Singapore.1252
[4] LC_NUMERIC=C LC_TIME=English_Singapore.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicAlignments_1.24.0 Rsamtools_2.4.0 Biostrings_2.56.0 XVector_0.28.0
[5] SummarizedExperiment_1.18.1 DelayedArray_0.14.0 matrixStats_0.56.0 Biobase_2.48.0
[9] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[13] BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] rstudioapi_0.11 zlibbioc_1.34.0 BiocParallel_1.22.0 lattice_0.20-41 tools_4.0.0
[6] grid_4.0.0 crayon_1.3.4 Matrix_1.2-18 GenomeInfoDbData_1.2.3 rtracklayer_1.48.0
[11] bitops_1.0-6 RCurl_1.98-1.2 compiler_4.0.0 XML_3.99-0.3
proActivthrows an error if input file is a xz-compressed TopHat2 junction BED file (.bed.xz). This behaviour stems fromreadTopHatJunctions(GenomicAlignmentspackage).Session info: