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lijingya / ELMER

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
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promoterMeth bug ? #20

Open Al3n70rn opened 5 years ago

Al3n70rn commented 5 years ago

When I try to use promoterMeth using different MAE, I get this error:

data(elmer.data.example.promoter)

Gene.promoter <- promoterMeth(mae.promoter)

|==============================================================================================================|100%                      
Completed after 0 s 
Error in `[.data.frame`(out, , c("GeneID", "Symbol", "Raw.p")) : undefined columns selected

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.3.so

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8    LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DT_0.7                      dplyr_0.8.3                 magrittr_1.5                RTCGA_1.14.0               
 [5] tidyr_0.8.3                 TCGAbiolinks_2.12.3         ELMER_2.8.0                 ELMER.data_2.8.0           
 [9] MultiAssayExperiment_1.10.4 SummarizedExperiment_1.14.0 DelayedArray_0.10.0         BiocParallel_1.18.0        
[13] matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0        GenomeInfoDb_1.20.0        
[17] IRanges_2.18.1              S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
  [1] R.utils_2.9.0               tidyselect_0.2.5            RSQLite_2.1.1               AnnotationDbi_1.46.0       
  [5] htmlwidgets_1.3             grid_3.6.0                  DESeq_1.36.0                munsell_0.5.0              
  [9] codetools_0.2-16            colorspace_1.4-1            knitr_1.23                  rstudioapi_0.10            
 [13] ggsignif_0.5.0              labeling_0.3                rstan_2.19.2                GenomeInfoDbData_1.2.1     
 [17] hwriter_1.3.2               KMsurv_0.1-5                bit64_0.9-7                 downloader_0.4             
 [21] vctrs_0.2.0                 generics_0.0.2              xfun_0.8                    biovizBase_1.32.0          
 [25] ggthemes_4.2.0              EDASeq_2.18.0               R6_2.4.0                    doParallel_1.0.14          
 [29] clue_0.3-57                 locfit_1.5-9.1              AnnotationFilter_1.8.0      bitops_1.0-6               
 [33] reshape_0.8.8               assertthat_0.2.1            scales_1.0.0                nnet_7.3-12                
 [37] gtable_0.3.0                sva_3.32.1                  processx_3.4.0              ensembldb_2.8.0            
 [41] rlang_0.4.0                 zeallot_0.1.0               genefilter_1.66.0           cmprsk_2.2-8               
 [45] GlobalOptions_0.1.0         splines_3.6.0               rtracklayer_1.44.0          lazyeval_0.2.2             
 [49] acepack_1.4.1               dichromat_2.0-0             selectr_0.4-1               broom_0.5.2                
 [53] checkmate_1.9.4             inline_0.3.15               GenomicFeatures_1.36.4      backports_1.1.4            
 [57] rsconnect_0.8.13            Hmisc_4.2-0                 tools_3.6.0                 ggplot2_3.2.0              
 [61] RColorBrewer_1.1-2          Rcpp_1.0.1                  plyr_1.8.4                  base64enc_0.1-3            
 [65] progress_1.2.2              zlibbioc_1.30.0             purrr_0.3.2                 RCurl_1.95-4.12            
 [69] ps_1.3.0                    prettyunits_1.0.2           ggpubr_0.2.1                rpart_4.1-15               
 [73] GetoptLong_0.1.7            viridis_0.5.1               zoo_1.8-6                   ggrepel_0.8.1              
 [77] cluster_2.1.0               data.table_1.12.2           circlize_0.4.6              survminer_0.4.4            
 [81] ProtGenerics_1.16.0         aroma.light_3.14.0          hms_0.5.0                   evaluate_0.14              
 [85] xtable_1.8-4                XML_3.98-1.20               gridExtra_2.3               shape_1.4.4                
 [89] compiler_3.6.0              biomaRt_2.40.1              tibble_2.1.3                crayon_1.3.4               
 [93] R.oo_1.22.0                 StanHeaders_2.18.1-10       htmltools_0.3.6             mgcv_1.8-28                
 [97] Formula_1.2-3               geneplotter_1.62.0          DBI_1.0.0                   matlab_1.0.2               
[101] ComplexHeatmap_2.0.0        ShortRead_1.42.0            Matrix_1.2-17               readr_1.3.1                
[105] cli_1.1.0                   R.methodsS3_1.7.1           Gviz_1.28.0                 pkgconfig_2.0.2            
[109] km.ci_0.5-2                 GenomicAlignments_1.20.1    foreign_0.8-71              plotly_4.9.0               
[113] xml2_1.2.0                  foreach_1.4.4               annotate_1.62.0             XVector_0.24.0             
[117] rvest_0.3.4                 stringr_1.4.0               VariantAnnotation_1.30.1    callr_3.3.0                
[121] digest_0.6.20               ConsensusClusterPlus_1.48.0 Biostrings_2.52.0           rmarkdown_1.14             
[125] survMisc_0.5.5              htmlTable_1.13.1            edgeR_3.26.5                curl_3.3                   
[129] Rsamtools_2.0.0             rjson_0.2.20                nlme_3.1-140                jsonlite_1.6               
[133] viridisLite_0.3.0           limma_3.40.2                BSgenome_1.52.0             pillar_1.4.2               
[137] lattice_0.20-38             loo_2.1.0                   httr_1.4.0                  pkgbuild_1.0.3             
[141] survival_2.44-1.1           glue_1.3.1                  png_0.1-7                   iterators_1.0.10           
[145] bit_1.1-14                  stringi_1.4.3               blob_1.2.0                  latticeExtra_0.6-28

Could you help me ?

Best regards, Agusti

Al3n70rn commented 5 years ago

Just an update, I have exactly the same error with R 3.6.1

Best, Agusti