[Bioc-devel] gwaswloc class broken
Robert Castelo
robert.castelo at upf.edu
Tue Feb 20 14:01:43 CET 2018
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
>
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>
--
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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