[Bioc-devel] gwaswloc class broken
Vincent Carey
stvjc at channing.harvard.edu
Tue Feb 20 15:41:41 CET 2018
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.castelo at 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.castelo at upf.edu
>> <mailto:robert.castelo at 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 at r-project.org <mailto:Bioc-devel at 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
>
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