Re: [Bioc-devel] Bioc-devel changes and SummarizedExperiment class
Thanks Hervé! Leonard On Tue, Apr 10, 2018 at 11:03 AM, Hervé Pagès 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-8LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] SGSeq_1.13.5SummarizedExperiment_1.9.16 >> [3] DelayedArray_0.5.23 BiocParallel_1.13.3 >> [5] matrixStats_0.53.1 Biobase_2.39.2 >> [7] Rsamtools_1.31.3Biostrings_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_1.1-13RSQLite_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_1.1.0rtracklayer_1.39.9 >> [21] httr_1.3.1stringr_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
Re: [Bioc-devel] Bioc-devel changes and SummarizedExperiment class
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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SGSeq_1.13.5SummarizedExperiment_1.9.16 [3] DelayedArray_0.5.23 BiocParallel_1.13.3 [5] matrixStats_0.53.1 Biobase_2.39.2 [7] Rsamtools_1.31.3Biostrings_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_1.1-13RSQLite_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_1.1.0rtracklayer_1.39.9 [21] httr_1.3.1stringr_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.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qpgk0XNxCYLZKHMRS-PnHD2znDDwj1P-Eiu7P4aUSuI&s=qjwH7TgvfYKGtMDCI77_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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioc-devel changes and SummarizedExperiment class
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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SGSeq_1.13.5SummarizedExperiment_1.9.16 [3] DelayedArray_0.5.23 BiocParallel_1.13.3 [5] matrixStats_0.53.1 Biobase_2.39.2 [7] Rsamtools_1.31.3Biostrings_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_1.1-13RSQLite_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_1.1.0rtracklayer_1.39.9 [21] httr_1.3.1stringr_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