Closed yujung-c closed 2 years ago
Please, update to the latest version:
BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")
Hi, Thank for the quick response. The issue is solved. =D
Hi , I encountered an issue that combining process fails since the length of columns in three files are different. Please help.
Objective Combine "Simple somatic mutation" from three maf files
Code
Screenshot or illustration
Error ################################################################ Error: Files must all have 90 columns:
File 2 has 91 columns ################################################################
packageVersion
packageVersion("TCGAbiolinks") [1] '2.22.4'
R version details
```R R.Version() $platform [1] "x86_64-redhat-linux-gnu" $arch [1] "x86_64" $os [1] "linux-gnu" $system [1] "x86_64, linux-gnu" $status [1] "" $major [1] "4" $minor [1] "1.3" $year [1] "2022" $month [1] "03" $day [1] "10" $`svn rev` [1] "81868" $language [1] "R" $version.string [1] "R version 4.1.3 (2022-03-10)" $nickname [1] "One Push-Up" ```R session information
```R > sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Fedora Linux 35 (Workstation Edition) Matrix products: default BLAS/LAPACK: /usr/lib64/libflexiblas.so.3.1 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel grid stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] UCSCXenaTools_1.4.7 sesame_1.12.9 sesameData_1.12.0 [4] rmarkdown_2.14 ExperimentHub_2.2.1 AnnotationHub_3.2.2 [7] BiocFileCache_2.2.1 dbplyr_2.1.1 DT_0.22 [10] ComplexHeatmap_2.11.1 tibble_3.1.6 dplyr_1.0.8 [13] maftools_2.10.05 tidyr_1.2.0 ELMER_2.18.0 [16] ELMER.data_2.18.0 Bioc2017.TCGAbiolinks.ELMER_0.0.0.9000 MultiAssayExperiment_1.20.0 [19] SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1 [22] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 [25] BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.62.0 [28] TCGAbiolinks_2.22.4 loaded via a namespace (and not attached): [1] rappdirs_0.3.3 rtracklayer_1.54.0 R.methodsS3_1.8.1 ggplot2_3.3.5 [5] bit64_4.0.5 knitr_1.38 DelayedArray_0.20.0 R.utils_2.11.0 [9] data.table_1.14.2 rpart_4.1.16 KEGGREST_1.34.0 RCurl_1.98-1.6 [13] AnnotationFilter_1.18.0 doParallel_1.0.17 generics_0.1.2 GenomicFeatures_1.46.5 [17] preprocessCore_1.56.0 RSQLite_2.2.12 proxy_0.4-26 bit_4.0.4 [21] tzdb_0.3.0 xml2_1.3.3 httpuv_1.6.5 assertthat_0.2.1 [25] xfun_0.30 hms_1.1.1 jquerylib_0.1.4 evaluate_0.15 [29] DNAcopy_1.68.0 promises_1.2.0.1 fansi_1.0.3 restfulr_0.0.13 [33] progress_1.2.2 DBI_1.1.2 htmlwidgets_1.5.4 reshape_0.8.9 [37] matlab_1.0.2 purrr_0.3.4 ellipsis_0.3.2 crosstalk_1.2.0 [41] ggpubr_0.4.0 backports_1.4.1 biomaRt_2.50.3 vctrs_0.4.1 [45] ensembldb_2.18.4 Cairo_1.5-15 abind_1.4-5 cachem_1.0.6 [49] withr_2.5.0 Gviz_1.38.4 BSgenome_1.62.0 checkmate_2.1.0 [53] vroom_1.5.7 GenomicAlignments_1.30.0 prettyunits_1.1.1 cluster_2.1.3 [57] DOSE_3.20.1 lazyeval_0.2.2 crayon_1.5.1 pkgconfig_2.0.3 [61] ProtGenerics_1.26.0 nnet_7.3-17 rlang_1.0.2 lifecycle_1.0.1 [65] downloader_0.4 filelock_1.0.2 dichromat_2.0-0 randomForest_4.7-1 [69] Matrix_1.4-1 carData_3.0-5 base64enc_0.1-3 GlobalOptions_0.1.2 [73] pheatmap_1.0.12 png_0.1-7 viridisLite_0.4.0 rjson_0.2.21 [77] bitops_1.0-7 R.oo_1.24.0 KernSmooth_2.23-20 Biostrings_2.62.0 [81] blob_1.2.3 shape_1.4.6 stringr_1.4.0 qvalue_2.26.0 [85] readr_2.1.2 jpeg_0.1-9 rstatix_0.7.0 ggsignif_0.6.3 [89] scales_1.2.0 memoise_2.0.1 magrittr_2.0.3 plyr_1.8.7 [93] zlibbioc_1.40.0 compiler_4.1.3 BiocIO_1.4.0 RColorBrewer_1.1-3 [97] clue_0.3-60 Rsamtools_2.10.0 cli_3.3.0 XVector_0.34.0 [101] patchwork_1.1.1 htmlTable_2.4.0 Formula_1.2-4 tidyselect_1.1.2 [105] stringi_1.7.6 TCGAbiolinksGUI.data_1.15.1 highr_0.9 yaml_2.3.5 [109] GOSemSim_2.20.0 latticeExtra_0.6-29 ggrepel_0.9.1 sass_0.4.1 [113] VariantAnnotation_1.40.0 fastmatch_1.1-3 tools_4.1.3 circlize_0.4.14 [117] rstudioapi_0.13 foreach_1.5.2 foreign_0.8-82 gridExtra_2.3 [121] ComplexUpset_1.3.3 digest_0.6.29 BiocManager_1.30.17 shiny_1.7.1.9003 [125] wheatmap_0.2.0 Rcpp_1.0.8.3 car_3.0-12 broom_0.8.0 [129] BiocVersion_3.14.0 later_1.3.0 httr_1.4.2 AnnotationDbi_1.56.2 [133] biovizBase_1.42.0 colorspace_2.0-3 rvest_1.0.2 XML_3.99-0.9 [137] splines_4.1.3 plotly_4.10.0 xtable_1.8-4 jsonlite_1.8.0 [141] R6_2.5.1 Hmisc_4.7-0 pillar_1.7.0 htmltools_0.5.2 [145] mime_0.12 glue_1.6.2 fastmap_1.1.0 BiocParallel_1.28.3 [149] class_7.3-20 interactiveDisplayBase_1.32.0 codetools_0.2-18 fgsea_1.20.0 [153] utf8_1.2.2 lattice_0.20-45 bslib_0.3.1 curl_4.3.2 [157] zip_2.2.0 GO.db_3.14.0 openxlsx_4.2.5 survival_3.3-1 [161] munsell_0.5.0 e1071_1.7-9 DO.db_2.9 GetoptLong_1.0.5 [165] GenomeInfoDbData_1.2.7 iterators_1.0.14 reshape2_1.4.4 gtable_0.3.0 ```