Thanks Hervé! Leonard
On Tue, Apr 10, 2018 at 11:03 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Leonard, > > This should be fixed in SGSeq 1.13.6 (see commit > 5dc16968f7ea1a4b59595ebaabacca9a76699b80). > > Cheers, > H. > > > On 04/04/2018 09:23 AM, Leonard Goldstein wrote: > >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt >> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qp >> gk0XNxCYLZKHMRS-PnHD2znDDwj1P-Eiu7P4aUSuI&s=qjwH7TgvfYKGtMDC >> I77_VVUw8S-5PA6ctju8Jb3erUQ&e= >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
