Question

Unable to find an inherited method for function distanceToNearest for signature GRanges

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rbronste ▴ 60

@rbronste-12189

Last seen 4.5 years ago

Attempting to run chipenrich on sample data set:

chipenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = c('GOBP', 'GOCC', 'GOMF'), locusdef = "nearest_tss", qc_plots = FALSE, out_name = NULL, n_cores = 1)

Running into the following error after some processing:

Reading peaks from data.frame..
Constructing GRanges
Sorting GRanges
Reducing GRanges
Assigning peaks to genes with assign_peaks(...) ..
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘distanceToNearest’ for signature ‘"GRanges", "NULL"’
In addition: Warning messages:
1: In supported_genesets()$organism == organism & genesets %in% supported_genesets()$geneset :
  longer object length is not a multiple of shorter object length
2: In if (!file.exists(genesets)) { :
  the condition has length > 1 and only the first element will be used

chipenrich granges distancetonearest function dataframe • 4.5k views

ADD COMMENT • link 6.5 years ago rbronste ▴ 60

score 0 · Answer 1 · 2017-11-11

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rcavalca ▴ 140

@rcavalca-7718

Last seen 5.3 years ago

United States

Hello,

Unfortunately, I'm not able to reproduce this error. Can you please post yours and maybe that'll help? I'm running R 3.4.1, chipenrich 2.0.1, and chipenrich.data 2.0.0. I'm not seeing errors with this on the Bioconductor build system, and peaks_E2F4 is used in the build process, so I'm a bit confused as to why you're seeing this.

Thanks,

Raymond

ADD COMMENT • link 6.5 years ago rcavalca ▴ 140

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data(peaks_E2F4, package = 'chipenrich.data')

chipenrich(peaks_E2F4, genome = 'hg19', genesets = c('GOBP', 'GOCC', 'GOMF'), locusdef = "nearest_tss", qc_plots = FALSE, out_name = NULL, n_cores = 1)

And getting the following error:

Reading peaks from data.frame..
Constructing GRanges
Sorting GRanges
Reducing GRanges
Assigning peaks to genes with assign_peaks(...) ..
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘distanceToNearest’ for signature ‘"GRanges", "NULL"’

Running identical version of Bioconductor and packages to you...

ADD REPLY • link 6.5 years ago rbronste ▴ 60

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This is truly bizarre. I'm sorry, but I'm not sure what to do...

ADD REPLY • link 6.4 years ago rcavalca ▴ 140

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Try re-installing (via biocLite()) S4Vectors, IRanges, GenomicRanges.

ADD REPLY • link 6.4 years ago Martin Morgan 25k

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> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hexbin_1.27.1                           vsn_3.44.0                              BiocInstaller_1.26.1                   
 [4] pheatmap_1.0.8                          DESeq2_1.16.1                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [7] GenomicFeatures_1.28.5                  AnnotationDbi_1.38.2                    chipenrich_2.0.1                       
[10] ggplot2_2.2.1                           DiffBind_2.4.8                          SummarizedExperiment_1.6.5             
[13] DelayedArray_0.2.7                      matrixStats_0.52.2                      Biobase_2.36.2                         
[16] GenomicRanges_1.28.6                    GenomeInfoDb_1.12.3                     IRanges_2.10.5                         
[19] S4Vectors_0.14.7                        BiocGenerics_0.22.1                    

loaded via a namespace (and not attached):
  [1] backports_1.1.1          GOstats_2.42.0           Hmisc_4.0-3              plyr_1.8.4               lazyeval_0.2.1          
  [6] GSEABase_1.38.2          splines_3.4.1            BatchJobs_1.6            BiocParallel_1.10.1      TH.data_1.0-8           
 [11] amap_0.8-14              digest_0.6.12            htmltools_0.3.6          GO.db_3.4.1              gdata_2.18.0            
 [16] magrittr_1.5             checkmate_1.8.5          memoise_1.1.0            BBmisc_1.11              cluster_2.0.6           
 [21] limma_3.32.10            Biostrings_2.44.2        org.Rn.eg.db_3.4.1       readr_1.1.1              annotate_1.54.0         
 [26] systemPipeR_1.10.2       sandwich_2.4-0           fail_1.3                 colorspace_1.3-2         blob_1.1.0              
 [31] ggrepel_0.7.0            dplyr_0.7.4              RCurl_1.95-4.8           org.Mm.eg.db_3.4.1       graph_1.54.0            
 [36] genefilter_1.58.1        bindr_0.1                brew_1.0-6               survival_2.41-3          sendmailR_1.2-1         
 [41] zoo_1.8-0                glue_1.2.0               gtable_0.2.0             zlibbioc_1.22.0          XVector_0.16.0          
 [46] MatrixModels_0.4-1       rms_5.1-1                SparseM_1.77             scales_0.5.0             mvtnorm_1.0-6           
 [51] DBI_0.7                  edgeR_3.18.1             org.Dm.eg.db_3.4.1       Rcpp_0.12.13             xtable_1.8-2            
 [56] htmlTable_1.9            foreign_0.8-69           bit_1.1-12               preprocessCore_1.38.1    Formula_1.2-2           
 [61] AnnotationForge_1.18.2   htmlwidgets_0.9          httr_1.3.1               gplots_3.0.1             RColorBrewer_1.1-2      
 [66] acepack_1.4.1            pkgconfig_2.0.1          XML_3.98-1.9             nnet_7.3-12              locfit_1.5-9.1          
 [71] labeling_0.3             rlang_0.1.4              org.Dr.eg.db_3.4.1       munsell_0.4.3            tools_3.4.1             
 [76] RSQLite_2.0              devtools_1.13.3          stringr_1.2.0            org.Hs.eg.db_3.4.1       knitr_1.17              
 [81] bit64_0.9-7              caTools_1.17.1           bindrcpp_0.2             RBGL_1.52.0              nlme_3.1-131            
 [86] chipenrich.data_2.0.0    quantreg_5.34            biomaRt_2.32.1           compiler_3.4.1           curl_3.0                
 [91] affyio_1.46.0            tibble_1.3.4             geneplotter_1.54.0       stringi_1.1.5            lattice_0.20-35         
 [96] Matrix_1.2-11            data.table_1.10.4-3      bitops_1.0-6             rtracklayer_1.36.6       R6_2.2.2                
[101] latticeExtra_0.6-28      affy_1.54.0              hwriter_1.3.2            ShortRead_1.34.2         KernSmooth_2.23-15      
[106] gridExtra_2.3            codetools_0.2-15         polspline_1.1.12         MASS_7.3-47              gtools_3.5.0            
[111] assertthat_0.2.0         Category_2.42.1          rjson_0.2.15             withr_2.1.0              GenomicAlignments_1.12.2
[116] Rsamtools_1.28.0         multcomp_1.4-8           GenomeInfoDbData_0.99.0  mgcv_1.8-22              hms_0.3                 
[121] grid_3.4.1               rpart_4.1-11             git2r_0.19.0             base64enc_0.1-3

ADD REPLY • link 6.5 years ago rbronste ▴ 60