Hello,

I'm attempting to use MethylAid on some Illumina 450k data, and am unable to run the visualize() function on the output of the summarize() function. i.e.: 

>library(MethylAid)
>sData <- summarize(targets)
Start summarization ...
Summarize data in one go...
Prepare data for plotting ...
... Finished summarization.
>outliers <- visualize(sData)

results in the following error:

Listening on http://127.0.0.1:5555
Warning in rm(list = "location", envir = globalenv()) :
  object 'location' not found
Warning: Error in : object of type 'closure' is not subsettable
Stack trace (innermost first):
    46: setHighlight
    45: plotMU
    44: <Anonymous>
    43: do.call
    42: initialize
    41: server
     3: runApp
     2: visualize
     1: visualize
Error : object of type 'closure' is not subsettable
ERROR: [on_request_read] connection reset by peer

I have MethylAid version 1.10.0, and shiny version 1.0.5. I'm using Rstudio 1.0.153.

Any help would be appreciated.

-- Andrew Mashchak

Loma Linda University / Adventist Health Study-2 / Biostatistician

The output of sessionInfo is:

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] IlluminaHumanMethylation450kmanifest_0.4.0
 [2] BiocParallel_1.10.1                       
 [3] DNAmArray_0.1.1                           
 [4] minfi_1.22.1                              
 [5] bumphunter_1.16.0                         
 [6] locfit_1.5-9.1                            
 [7] iterators_1.0.8                           
 [8] foreach_1.4.3                             
 [9] Biostrings_2.44.2                         
[10] XVector_0.16.0                            
[11] SummarizedExperiment_1.6.5                
[12] DelayedArray_0.2.7                        
[13] matrixStats_0.52.2                        
[14] FDb.InfiniumMethylation.hg19_2.2.0        
[15] org.Hs.eg.db_3.4.1                        
[16] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2   
[17] GenomicFeatures_1.28.5                    
[18] AnnotationDbi_1.38.2                      
[19] Biobase_2.36.2                            
[20] GenomicRanges_1.28.5                      
[21] GenomeInfoDb_1.12.2                       
[22] IRanges_2.10.3                            
[23] S4Vectors_0.14.5                          
[24] BiocGenerics_0.22.0                       
[25] devtools_1.13.3                           
[26] shiny_1.0.5                               
[27] MethylAid_1.10.0                          
[28] magrittr_1.5                              
[29] dplyr_0.7.4                               

loaded via a namespace (and not attached):
 [1] nlme_3.1-131             bitops_1.0-6            
 [3] bit64_0.9-7              RColorBrewer_1.1-2      
 [5] httr_1.3.1               tools_3.4.1             
 [7] doRNG_1.6.6              nor1mix_1.2-3           
 [9] R6_2.2.2                 DBI_0.7                 
[11] lazyeval_0.2.0           colorspace_1.3-2        
[13] withr_2.0.0              base64_2.0              
[15] curl_2.8.1               git2r_0.19.0            
[17] bit_1.1-12               compiler_3.4.1          
[19] preprocessCore_1.38.1    pkgmaker_0.22           
[21] rtracklayer_1.36.4       scales_0.5.0            
[23] hexbin_1.27.1            genefilter_1.58.1       
[25] quadprog_1.5-5           stringr_1.2.0           
[27] digest_0.6.12            Rsamtools_1.28.0        
[29] illuminaio_0.18.0        siggenes_1.50.0         
[31] GEOquery_2.42.0          pkgconfig_2.0.1         
[33] htmltools_0.3.6          limma_3.32.7            
[35] rlang_0.1.2              RSQLite_2.0             
[37] bindr_0.1                jsonlite_1.5            
[39] mclust_5.3               RCurl_1.95-4.8          
[41] GenomeInfoDbData_0.99.0  Matrix_1.2-11           
[43] Rcpp_0.12.13             munsell_0.4.3           
[45] stringi_1.1.5            MASS_7.3-47             
[47] zlibbioc_1.22.0          plyr_1.8.4              
[49] grid_3.4.1               blob_1.1.0              
[51] lattice_0.20-35          splines_3.4.1           
[53] multtest_2.32.0          annotate_1.54.0         
[55] beanplot_1.2             rngtools_1.2.4          
[57] codetools_0.2-15         biomaRt_2.32.1          
[59] XML_3.98-1.9             glue_1.1.1              
[61] data.table_1.10.4        httpuv_1.3.5            
[63] gtable_0.2.0             openssl_0.9.7           
[65] reshape_0.8.7            assertthat_0.2.0        
[67] ggplot2_2.2.1            gridBase_0.4-7          
[69] mime_0.5                 xtable_1.8-2            
[71] survival_2.41-3          tibble_1.3.4            
[73] GenomicAlignments_1.12.2 registry_0.3            
[75] memoise_1.1.0            bindrcpp_0.2 

Hi Andrew,

Are you able to run the example see ?summarize and use visualize(data).  I'm able to run it without any problems using MethylAid version 1.10.0 and shiny version 1.0.5 on Ubuntu using emacs.

Could you compare str(data) from the example with your summarized data. It seems that the initialization of the shiny didn't work properly. Or you could sent me the summarized object and I'll look at it.

Cheers,

Maarten