________________________________________
From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Nicolas Delhomme [nicolas.delhomme at umu.se]
Sent: Sunday, December 20, 2015 3:10 AM
To: Bioc-devel at r-project.org
Subject: [Bioc-devel] as.table not available for HitsList anymore?
Hej Herv? (I guess that ones for you :-)!
In R dev / Bioc 3.3; calling as.table on an HitsList stopped working:
Browse[2]> ovl
HitsList of length 6
names(6): chr2L chr2R chr3L chr3R chr4 chrX
Browse[2]> as.table(ovl)
Error during wrapup: cannot coerce to a table
I suppose this may have to do with the refactoring of the IRanges/S4Vectors packages? Will the functionality be re-instated, or should I switch my code to using as.matrix instead?
My session info:
R Under development (unstable) (2015-12-15 r69777)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RnaSeqTutorial_0.9.0 easyRNASeq_2.7.2
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 futile.logger_1.4.1
[3] GenomeInfoDb_1.7.3 XVector_0.11.1
[5] futile.options_1.0.0 bitops_1.0-6
[7] tools_3.3.0 zlibbioc_1.17.0
[9] biomaRt_2.27.2 annotate_1.49.0
[11] RSQLite_1.0.0 lattice_0.20-33
[13] DBI_0.3.1 parallel_3.3.0
[15] DESeq_1.23.0 genefilter_1.53.0
[17] hwriter_1.3.2 Biostrings_2.39.3
[19] S4Vectors_0.9.15 IRanges_2.5.18
[21] locfit_1.5-9.1 stats4_3.3.0
[23] grid_3.3.0 LSD_3.0
[25] Biobase_2.31.3 AnnotationDbi_1.33.3
[27] XML_3.98-1.3 survival_2.38-3
[29] BiocParallel_1.5.1 limma_3.27.6
[31] latticeExtra_0.6-26 geneplotter_1.49.0
[33] lambda.r_1.1.7 edgeR_3.13.4
[35] intervals_0.15.1 Rsamtools_1.23.1
[37] genomeIntervals_1.27.0 splines_3.3.0
[39] BiocGenerics_0.17.2 GenomicAlignments_1.7.3
[41] GenomicRanges_1.23.7 ShortRead_1.29.1
[43] SummarizedExperiment_1.1.11 xtable_1.8-0
[45] RCurl_1.95-4.7
Thanks!
Nico
PS Have a good Christmas time!
---------------------------------------------------------------
Nicolas Delhomme, PhD
Acting Manager
UPSC bioinformatics core facility
Ume? Plant Science Center,
Swedish University for Agricultural
Sciences (SLU) and Ume? University
Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Ume? universitet
Ume? S-901 87 Sweden
---------------------------------------------------------------
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