Error using minfi::plotSex in methyl/minfi.Rmd

[gillsignals]

The second to last line of methyl/minfi.Rmd generates an error:

> plotSex(sex)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'colData' for signature '"DataFrame"'

I implemented some small fixes to this document in a PR to fix some deprecated functions which you may wish to apply first. I do not know where this DataFrame error comes from.

The session info is below. Thanks!

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 IlluminaHumanMethylation450kmanifest_0.4.0        
 [3] minfi_1.30.0                                       HistData_0.8-4                                    
 [5] broom_0.5.2                                        Lahman_7.0-1                                      
 [7] tidytext_0.2.2                                     gutenbergr_0.1.4                                  
 [9] rvest_0.3.4                                        xml2_1.2.2                                        
[11] bumphunter_1.26.0                                  locfit_1.5-9.1                                    
[13] iterators_1.0.12                                   foreach_1.4.7                                     
[15] limma_3.40.6                                       coloncancermeth_1.0                               
[17] cummeRbund_2.26.0                                  Gviz_1.28.1                                       
[19] rtracklayer_1.44.2                                 fastcluster_1.1.25                                
[21] reshape2_1.4.3                                     RSQLite_2.1.2                                     
[23] DEXSeq_1.30.0                                      RColorBrewer_1.1-2                                
[25] pasilla_1.12.0                                     sva_3.32.1                                        
[27] genefilter_1.66.0                                  mgcv_1.8-28                                       
[29] nlme_3.1-141                                       org.Hs.eg.db_3.8.2                                
[31] pheatmap_1.0.12                                    vsn_3.52.0                                        
[33] DESeq2_1.24.0                                      rafalib_1.0.0                                     
[35] GenomicAlignments_1.20.1                           Rsamtools_2.0.0                                   
[37] Biostrings_2.52.0                                  XVector_0.24.0                                    
[39] airway_1.4.0                                       SummarizedExperiment_1.14.1                       
[41] DelayedArray_0.10.0                                BiocParallel_1.18.1                               
[43] matrixStats_0.54.0                                 forcats_0.4.0                                     
[45] stringr_1.4.0                                      dplyr_0.8.3                                       
[47] purrr_0.3.2                                        readr_1.3.1                                       
[49] tidyr_0.8.3                                        tibble_2.1.3                                      
[51] tidyverse_1.2.1                                    dslabs_0.7.1                                      
[53] Cen.ele6_1.0.0                                     TxDb.Celegans.UCSC.ce6.ensGene_3.2.2              
[55] org.Ce.eg.db_3.8.2                                 GO.db_3.8.2                                       
[57] OrganismDbi_1.26.0                                 GenomicFeatures_1.36.4                            
[59] AnnotationDbi_1.46.1                               Biobase_2.44.0                                    
[61] GenomicRanges_1.36.0                               GenomeInfoDb_1.20.0                               
[63] IRanges_2.18.1                                     S4Vectors_0.22.0                                  
[65] ERBS_1.0                                           erbsViz_0.0.0.9000                                
[67] juxtaPack_0.0.0.9000                               ggbio_1.32.0                                      
[69] ggplot2_3.2.1                                      BiocGenerics_0.30.0                               
[71] usethis_1.5.1                                     

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1           SnowballC_0.6.0          GGally_1.4.0             pkgmaker_0.27            acepack_1.4.1           
  [6] bit64_0.9-7              knitr_1.24               data.table_1.12.2        rpart_4.1-15             hwriter_1.3.2           
 [11] GEOquery_2.52.0          RCurl_1.95-4.12          AnnotationFilter_1.8.0   generics_0.0.2           snow_0.4-3              
 [16] preprocessCore_1.46.0    callr_3.3.1              commonmark_1.7           bit_1.1-14               tokenizers_0.2.1        
 [21] lubridate_1.7.4          assertthat_0.2.1         xfun_0.9                 hms_0.5.1                scrime_1.3.5            
 [26] fansi_0.4.0              progress_1.2.2           readxl_1.3.1             DBI_1.0.0                geneplotter_1.62.0      
 [31] htmlwidgets_1.3          reshape_0.8.8            selectr_0.4-1            backports_1.1.4          annotate_1.62.0         
 [36] textdata_0.3.0           biomaRt_2.40.4           vctrs_0.2.0              remotes_2.1.0            ensembldb_2.8.0         
 [41] withr_2.1.2              triebeard_0.3.0          BSgenome_1.52.0          checkmate_1.9.4          prettyunits_1.0.2       
 [46] mclust_5.4.5             cluster_2.1.0            lazyeval_0.2.2           crayon_1.3.4             pkgconfig_2.0.2         
 [51] labeling_0.3             pkgload_1.0.2            ProtGenerics_1.16.0      nnet_7.3-12              devtools_2.1.0          
 [56] rlang_0.4.0              registry_0.5-1           affyio_1.54.0            modelr_0.1.5             dichromat_2.0-0         
 [61] cellranger_1.1.0         rprojroot_1.3-2          graph_1.62.0             rngtools_1.4             base64_2.0              
 [66] Matrix_1.2-17            urltools_1.7.3           Rhdf5lib_1.6.0           base64enc_0.1-3          whisker_0.4             
 [71] processx_3.4.1           clisymbols_1.2.0         bitops_1.0-6             DelayedMatrixStats_1.6.0 blob_1.2.0              
 [76] doRNG_1.7.1              nor1mix_1.3-0            scales_1.0.0             memoise_1.1.0            magrittr_1.5            
 [81] plyr_1.8.4               hexbin_1.27.3            bibtex_0.4.2             zlibbioc_1.30.0          compiler_3.6.1          
 [86] illuminaio_0.26.0        cli_1.1.0                affy_1.62.0              janeaustenr_0.1.5        ps_1.3.0                
 [91] htmlTable_1.13.1         Formula_1.2-3            MASS_7.3-51.4            tidyselect_0.2.5         stringi_1.4.3           
 [96] askpass_1.1              latticeExtra_0.6-28      VariantAnnotation_1.30.1 tools_3.6.1              rstudioapi_0.10         
[101] foreign_0.8-71           git2r_0.26.1             gridExtra_2.3            digest_0.6.20            BiocManager_1.30.4      
[106] quadprog_1.5-7           Rcpp_1.0.1               siggenes_1.58.0          httr_1.4.1               biovizBase_1.32.0       
[111] colorspace_1.4-1         XML_3.98-1.20            fs_1.3.1                 splines_3.6.1            RBGL_1.60.0             
[116] statmod_1.4.32           multtest_2.40.0          sessioninfo_1.1.1        xtable_1.8-4             jsonlite_1.6            
[121] zeallot_0.1.0            testthat_2.2.1           R6_2.4.0                 Hmisc_4.2-0              pillar_1.4.2            
[126] htmltools_0.3.6          glue_1.3.1               beanplot_1.2             codetools_0.2-16         pkgbuild_1.0.5          
[131] utf8_1.1.4               lattice_0.20-38          curl_4.0                 openssl_1.4.1            survival_2.44-1.1       
[136] roxygen2_6.1.1           desc_1.2.0               munsell_0.5.0            rhdf5_2.28.0             GenomeInfoDbData_1.2.1  
[141] HDF5Array_1.12.2         haven_2.1.1              gtable_0.3.0 

[gillsignals]

Issue can be closed once PR is accepted. Thanks!