Hi Hervé, Some recent changes in bioc-devel are causing trouble with SummarizedExperiment objects if the rowRanges slot inherits from GRangesList. Please see example below.
Thanks in advance for your help. Leonard -- > library(SGSeq) > > ## SGVariants object inherits from GRangesList > is(sgv_pred) [1] "SGVariants" "GRangesList" [3] "Paths" "GenomicRangesList" [5] "CompressedRangesList" "GenomicRanges_OR_GRangesList" [7] "RangesList" "CompressedList" [9] "GenomicRanges_OR_GenomicRangesList" "List" [11] "Vector" "list_OR_List" [13] "Annotated" > > ## example counts > counts <- matrix(1:2, ncol = 1) > > ## creating SummarizedExperiment object fails > SummarizedExperiment(assays = list(counts), rowRanges = sgv_pred) class: RangedSummarizedExperiment dim: 2 1 metadata(0): assays(1): '' Error in .local(object, ..., verbose) : unused argument (check = FALSE) > > ## works after coercing to GRangestList > SummarizedExperiment(assays = list(counts), rowRanges = as(sgv_pred, "GRangesList")) class: RangedSummarizedExperiment dim: 2 1 metadata(0): assays(1): '' rownames: NULL rowData names(20): from to ... variantType variantName colnames: NULL colData names(0): > > sessionInfo() R Under development (unstable) (2017-10-20 r73567) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago) Matrix products: default BLAS: /gnet/is2/p01/apps/R/3.5.0-20171105-devel/x86_64-linux-2.6-rhel6/lib64/R/lib/libRblas.so LAPACK: /gnet/is2/p01/apps/R/3.5.0-20171105-devel/x86_64-linux-2.6-rhel6/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SGSeq_1.13.5 SummarizedExperiment_1.9.16 [3] DelayedArray_0.5.23 BiocParallel_1.13.3 [5] matrixStats_0.53.1 Biobase_2.39.2 [7] Rsamtools_1.31.3 Biostrings_2.47.12 [9] XVector_0.19.9 GenomicRanges_1.31.23 [11] GenomeInfoDb_1.15.5 IRanges_2.13.28 [13] S4Vectors_0.17.39 BiocGenerics_0.25.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.16 compiler_3.5.0 [3] GenomicFeatures_1.31.10 prettyunits_1.0.2 [5] bitops_1.0-6 tools_3.5.0 [7] zlibbioc_1.25.0 progress_1.1.2 [9] biomaRt_2.35.13 digest_0.6.15 [11] bit_1.1-13 RSQLite_2.1.0 [13] memoise_1.1.0 lattice_0.20-35 [15] pkgconfig_2.0.1 igraph_1.2.1 [17] Matrix_1.2-13 DBI_0.8 [19] GenomeInfoDbData_1.1.0 rtracklayer_1.39.9 [21] httr_1.3.1 stringr_1.3.0 [23] bit64_0.9-8 grid_3.5.0 [25] R6_2.2.2 AnnotationDbi_1.41.4 [27] XML_3.98-1.10 blob_1.1.1 [29] magrittr_1.5 GenomicAlignments_1.15.13 [31] RUnit_0.4.31 assertthat_0.2.0 [33] stringi_1.1.7 RCurl_1.95-4.10 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel