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
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