I think this is settled by running updateObject(ebicat37) with a current GenomicRanges etc.
I will do this and reserialize. On Tue, Feb 20, 2018 at 8:01 AM, Robert Castelo <robert.cast...@upf.edu> wrote: > thanks Vince for your quick response, indeed your intuition is right, > coercing to 'GRanges' avoids the problem, i'm cc'ing bioc-devel so that > people involved in 'GRanges' know about this: > > library(gwascat) > data(ebicat37) > ebicat37[1] > Error in updateObject(x, check = FALSE) : > no slot of name "elementType" for this object of class "gwaswloc" > > ebicat37b <- as(ebicat37, "GRanges") > ebicat37b[1] > GRanges object with 1 range and 36 metadata columns: > seqnames ranges strand | DATE ADDED TO CATALOG PUBMEDID > <Rle> <IRanges> <Rle> | <character> <integer> > [1] chr11 41820450 * | 09-Jul-2015 26114229 > > [ ... more output ...] ## i'm typing this myself to keep the email short > > PLATFORM [SNPS PASSING QC] CNV > <character> <character> > [1] Illumina [up to 5,616,481] (imputed) N > MAPPED_TRAIT MAPPED_TRAIT_URI > <character> <character> > [1] post-traumatic stress disorder http://www.ebi.ac.uk/efo/EFO_0001358 > ------- > seqinfo: 23 sequences from GRCh37 genome > > > cheers, > > robert. > > On 02/20/2018 01:51 PM, Vincent Carey wrote: > >> thanks robert traveling but will tackle asap if u can coerce to >> granges it may help as the only purpose of gwaswloc is to have a concise >> show method but the coercion might fail too >> >> On Tue, Feb 20, 2018 at 6:43 AM Robert Castelo <robert.cast...@upf.edu >> <mailto:robert.cast...@upf.edu>> wrote: >> >> hi, >> >> the 'gwasloc' class from the gwascat package seems to be broken in >> devel, i suspect due to recent changes in the 'GRanges' class or some >> other class upstream, because the definition of the 'gwasloc' class in >> gwascat/R/classes.R is: >> >> setClass("gwaswloc", representation(extractDate="character"), >> contains="GRanges") >> >> i paste below a minimal example, traceback and (very long) >> corresponding >> session info. i'm using it in the vignette of GenomicScores, so it's >> not >> so crucial but it would be nice to have it working again. thanks!! >> >> library(gwascat) >> >> data(ebicat37) >> >> class(ebicat37) >> [1] "gwaswloc" >> attr(,"package") >> [1] "gwascat" >> >> ebicat37[1] >> Error in updateObject(x, check = FALSE) : >> no slot of name "elementType" for this object of class "gwaswloc" >> 9: updateObject(x, check = FALSE) >> 8: updateObject(x, check = FALSE) >> 7: extractROWS(x, i) >> 6: extractROWS(x, i) >> 5: subset_along_ROWS(x, i, , ..., drop = drop) >> 4: .nextMethod(x = x, i = i) >> 3: callNextMethod() >> 2: ebicat37[1] >> 1: ebicat37[1] >> sessionInfo() >> R Under development (unstable) (2017-10-30 r73642) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: CentOS Linux 7 (Core) >> >> Matrix products: default >> BLAS: /opt/R/R-devel/lib64/R/lib/libRblas.so >> LAPACK: /opt/R/R-devel/lib64/R/lib/libRlapack.so >> >> locale: >> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8 >> [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8 >> [7] LC_PAPER=en_US.UTF8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats4 stats graphics grDevices utils >> datasets >> [8] methods base >> >> other attached packages: >> [1] gwascat_2.11.1 >> [2] Homo.sapiens_1.3.1 >> [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 >> [4] org.Hs.eg.db_3.5.0 >> [5] GO.db_3.5.0 >> [6] OrganismDbi_1.21.1 >> [7] GenomicFeatures_1.31.10 >> [8] GenomicRanges_1.31.22 >> [9] GenomeInfoDb_1.15.5 >> [10] AnnotationDbi_1.41.4 >> [11] IRanges_2.13.26 >> [12] S4Vectors_0.17.33 >> [13] Biobase_2.39.2 >> [14] BiocGenerics_0.25.3 >> [15] colorout_1.1-3 >> >> loaded via a namespace (and not attached): >> [1] ggbeeswarm_0.6.0 colorspace_1.3-2 >> [3] biovizBase_1.27.1 htmlTable_1.11.2 >> [5] XVector_0.19.8 base64enc_0.1-3 >> [7] dichromat_2.0-0 rstudioapi_0.7 >> [9] bit64_0.9-7 interactiveDisplayBase_1.17.0 >> [11] codetools_0.2-15 splines_3.5.0 >> [13] snpStats_1.29.1 ggbio_1.27.1 >> [15] doParallel_1.0.11 knitr_1.19 >> [17] Formula_1.2-2 jsonlite_1.5 >> [19] gQTLBase_1.11.0 Rsamtools_1.31.3 >> [21] cluster_2.0.6 graph_1.57.1 >> [23] shiny_1.0.5 compiler_3.5.0 >> [25] httr_1.3.1 backports_1.1.2 >> [27] assertthat_0.2.0 Matrix_1.2-12 >> [29] lazyeval_0.2.1 limma_3.35.11 >> [31] acepack_1.4.1 htmltools_0.3.6 >> [33] prettyunits_1.0.2 tools_3.5.0 >> [35] bindrcpp_0.2 gtable_0.2.0 >> [37] glue_1.2.0 GenomeInfoDbData_1.1.0 >> [39] reshape2_1.4.3 dplyr_0.7.4 >> [41] fastmatch_1.1-0 Rcpp_0.12.15 >> [43] Biostrings_2.47.9 nlme_3.1-135.5 >> [45] rtracklayer_1.39.9 iterators_1.0.9 >> [47] ffbase_0.12.3 stringr_1.3.0 >> [49] mime_0.5 ensembldb_2.3.11 >> [51] XML_3.98-1.10 AnnotationHub_2.11.2 >> [53] zlibbioc_1.25.0 scales_0.5.0 >> [55] BSgenome_1.47.5 VariantAnnotation_1.25.12 >> [57] BiocInstaller_1.29.4 ProtGenerics_1.11.0 >> [59] SummarizedExperiment_1.9.14 RBGL_1.55.0 >> [61] AnnotationFilter_1.3.2 RColorBrewer_1.1-2 >> [63] BBmisc_1.11 yaml_2.1.16 >> [65] curl_3.1 memoise_1.1.0 >> [67] gridExtra_2.3 ggplot2_2.2.1 >> [69] rpart_4.1-12 biomaRt_2.35.10 >> [71] latticeExtra_0.6-28 reshape_0.8.7 >> [73] stringi_1.1.6 RSQLite_2.0 >> [75] foreach_1.4.4 RMySQL_0.10.13 >> [77] checkmate_1.8.5 BiocParallel_1.13.1 >> [79] rlang_0.1.6 pkgconfig_2.0.1 >> [81] BatchJobs_1.7 GenomicFiles_1.15.2 >> [83] matrixStats_0.53.1 bitops_1.0-6 >> [85] lattice_0.20-35 purrr_0.2.4 >> [87] bindr_0.1 GenomicAlignments_1.15.12 >> [89] htmlwidgets_1.0 bit_1.1-12 >> [91] GGally_1.3.2 plyr_1.8.4 >> [93] magrittr_1.5 sendmailR_1.2-1 >> [95] R6_2.2.2 Hmisc_4.1-1 >> [97] erma_0.11.6 DelayedArray_0.5.20 >> [99] DBI_0.7 foreign_0.8-70 >> [101] pillar_1.1.0 mgcv_1.8-23 >> [103] nnet_7.3-12 survival_2.41-3 >> [105] RCurl_1.95-4.10 tibble_1.4.2 >> [107] plotly_4.7.1 progress_1.1.2 >> [109] grid_3.5.0 data.table_1.10.4-3 >> [111] blob_1.1.0 gQTLstats_1.11.4 >> [113] digest_0.6.15 xtable_1.8-2 >> [115] ff_2.2-13 tidyr_0.8.0 >> [117] httpuv_1.3.5 brew_1.0-6 >> [119] munsell_0.4.3 beeswarm_0.2.3 >> [121] viridisLite_0.3.0 Gviz_1.23.3 >> [123] vipor_0.4.5 >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing >> list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > -- > Robert Castelo, PhD > Associate Professor > Dept. of Experimental and Health Sciences > Universitat Pompeu Fabra (UPF) > Barcelona Biomedical Research Park (PRBB) > Dr Aiguader 88 > E-08003 Barcelona, Spain > telf: +34.933.160.514 > fax: +34.933.160.550 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel