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Describe the issue filterMaf returns errors whenever I try to run it Command output:
Error in `[.data.table`(summary, , `:=`(Mean, vc.mean)) : Supplied 13 items to be assigned to 14 items of column 'Mean'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code. In addition: Warning message: Item 1 has 13 rows but longest item has 14; recycled with remainder.
Session info Run sessionInfo() and post the output below
sessionInfo()
R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.utf8 time zone: Europe/London tzcode source: internal attached base packages: [1] parallel grid stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] mclust_6.1.1 stringr_1.5.1 tidyr_1.3.1 [4] UpSetR_1.4.0 ChIPseeker_1.38.0 pheatmap_1.0.12 [7] EDASeq_2.36.0 ShortRead_1.60.0 GenomicAlignments_1.38.2 [10] Rsamtools_2.18.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0 DESeq2_1.42.1 [13] csaw_1.36.1 ChIPpeakAnno_3.36.1 clusterProfiler_4.10.1 [16] WGCNA_1.72-5 fastcluster_1.2.6 dynamicTreeCut_1.63-1 [19] dplyr_1.1.4 ggthemes_5.1.0 ggpubr_0.6.0 [22] ComplexHeatmap_2.18.0 circlize_0.4.16 sva_3.50.0 [25] BiocParallel_1.36.0 genefilter_1.84.0 mgcv_1.9-1 [28] nlme_3.1-164 statmod_1.5.0 RColorBrewer_1.1-3 [31] rgl_1.3.1 ggfortify_0.4.17 factoextra_1.0.7 [34] RnBeads_2.20.0 plyr_1.8.9 methylumi_2.48.0 [37] minfi_1.48.0 bumphunter_1.44.0 locfit_1.5-9.9 [40] iterators_1.0.14 foreach_1.5.2 Biostrings_2.70.2 [43] XVector_0.42.0 SummarizedExperiment_1.32.0 MatrixGenerics_1.14.0 [46] FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.18.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [49] GenomicFeatures_1.54.4 AnnotationDbi_1.64.1 reshape2_1.4.4 [52] scales_1.3.0 illuminaio_0.44.0 matrixStats_1.2.0 [55] gridExtra_2.3 gplots_3.1.3.1 fields_15.2 [58] viridisLite_0.4.2 spam_2.10-0 ff_4.0.12 [61] bit_4.0.5 cluster_2.1.6 MASS_7.3-60.0.1 [64] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0 [67] S4Vectors_0.40.2 maftools_2.18.0 ggrepel_0.9.5 [70] ggplot2_3.5.1 edgeR_4.0.16 limma_3.58.1 [73] Biobase_2.62.0 BiocGenerics_0.48.1 loaded via a namespace (and not attached): [1] igraph_2.0.3 graph_1.80.0 Formula_1.2-5 maps_3.4.2 [5] zlibbioc_1.48.0 tidyselect_1.2.1 doParallel_1.0.17 clue_0.3-65 [9] lattice_0.22-5 rjson_0.2.21 nor1mix_1.3-3 blob_1.2.4 [13] rngtools_1.5.2 S4Arrays_1.2.0 base64_2.0.1 dichromat_2.0-0.1 [17] scrime_1.3.5 png_0.1-8 plotrix_3.8-4 cli_3.6.2 [21] ggplotify_0.1.2 registry_0.5-1 ProtGenerics_1.34.0 askpass_1.2.0 [25] multtest_2.58.0 openssl_2.1.2 BiocIO_1.12.0 purrr_1.0.2 [29] shadowtext_0.1.3 curl_5.2.0 mime_0.12 evaluate_0.23 [33] tidytree_0.4.6 stringi_1.8.3 backports_1.4.1 XML_3.99-0.16.1 [37] httpuv_1.6.15 magrittr_2.0.3 rappdirs_0.3.3 splines_4.3.2 [41] KMsurv_0.1-5 jpeg_0.1-10 doRNG_1.8.6 ggraph_2.2.1 [45] survminer_0.4.9 DBI_1.2.2 HDF5Array_1.30.1 karyoploteR_1.28.0 [49] withr_3.0.0 enrichplot_1.22.0 RBGL_1.78.0 tidygraph_1.3.1 [53] formatR_1.14 bezier_1.1.2 rtracklayer_1.62.0 BiocManager_1.30.23 [57] htmlwidgets_1.6.4 fs_1.6.4 biomaRt_2.58.2 labeling_0.4.3 [61] SparseArray_1.2.3 annotate_1.80.0 VariantAnnotation_1.48.1 zoo_1.8-12 [65] knitr_1.46 beanplot_1.3.1 fansi_1.0.6 patchwork_1.2.0 [69] caTools_1.18.2 data.table_1.15.0 ggtree_3.10.1 rhdf5_2.46.1 [73] R.oo_1.26.0 regioneR_1.34.0 gridGraphics_0.5-1 aroma.light_3.32.0 [77] lazyeval_0.2.2 yaml_2.3.8 survival_3.5-7 BiocVersion_3.18.1 [81] crayon_1.5.2 tweenr_2.0.3 later_1.3.2 codetools_0.2-20 [85] base64enc_0.1-3 GlobalOptions_0.1.2 KEGGREST_1.42.0 shape_1.4.6.1 [89] filelock_1.0.3 foreign_0.8-86 pkgconfig_2.0.3 xml2_1.3.6 [93] aplot_0.2.2 BSgenome_1.70.2 ape_5.8 biovizBase_1.50.0 [97] gridBase_0.4-7 xtable_1.8-4 interp_1.1-6 hwriter_1.3.2.1 [101] car_3.1-2 httr_1.4.7 tools_4.3.2 globals_0.16.3 [105] htmlTable_2.4.2 broom_1.0.5 checkmate_2.3.1 futile.logger_1.4.3 [109] lambda.r_1.2.4 sigminer_2.3.0 HDO.db_0.99.1 dbplyr_2.5.0 [113] survMisc_0.5.6 digest_0.6.34 Matrix_1.6-5 furrr_0.3.1 [117] farver_2.1.1 tzdb_0.4.0 AnnotationFilter_1.26.0 yulab.utils_0.1.4 [121] viridis_0.6.5 rpart_4.1.23 glue_1.7.0 cachem_1.0.8 [125] VennDiagram_1.7.3 BiocFileCache_2.10.2 polyclip_1.10-6 Hmisc_5.1-1 [129] generics_0.1.3 parallelly_1.37.1 pkgload_1.3.4 impute_1.76.0 [133] GEOquery_2.70.0 carData_3.0-5 gson_0.1.0 utf8_1.2.4 [137] siggenes_1.76.0 graphlayouts_1.1.1 gtools_3.9.5 bamsignals_1.34.0 [141] preprocessCore_1.64.0 ggsignif_0.6.4 shiny_1.8.1.1 GenomeInfoDbData_1.2.11 [145] R.utils_2.12.3 rhdf5filters_1.14.1 RCurl_1.98-1.14 memoise_2.0.1 [149] rmarkdown_2.26 chromoMap_4.1.1 R.methodsS3_1.8.2 future_1.33.2 [153] reshape_0.8.9 km.ci_0.5-6 rstudioapi_0.16.0 hms_1.1.3 [157] munsell_0.5.1 cowplot_1.1.3 colorspace_2.1-0 rlang_1.1.3 [161] quadprog_1.5-8 DelayedMatrixStats_1.24.0 sparseMatrixStats_1.14.0 dotCall64_1.1-1 [165] ggforce_0.4.2 xfun_0.43 abind_1.4-5 GOSemSim_2.28.1 [169] tibble_3.2.1 interactiveDisplayBase_1.40.0 treeio_1.26.0 Rhdf5lib_1.24.2 [173] readr_2.1.5 futile.options_1.0.1 bitops_1.0-7 promises_1.3.0 [177] InteractionSet_1.30.0 scatterpie_0.2.2 RSQLite_2.3.5 qvalue_2.34.0 [181] fgsea_1.28.0 DelayedArray_0.28.0 GO.db_3.18.0 compiler_4.3.2 [185] prettyunits_1.2.0 boot_1.3-30 listenv_0.9.1 Rcpp_1.0.12 [189] DNAcopy_1.76.0 AnnotationHub_3.10.1 progress_1.2.3 R6_2.5.1 [193] fastmap_1.1.1 fastmatch_1.1-4 rstatix_0.7.2 ensembldb_2.26.0 [197] nnet_7.3-19 gtable_0.3.5 KernSmooth_2.23-22 latticeExtra_0.6-30 [201] deldir_2.0-4 htmltools_0.5.7 bit64_4.0.5 lifecycle_1.0.4 [205] restfulr_0.0.15 vctrs_0.6.5 DOSE_3.28.2 NMF_0.27 [209] ggfun_0.1.4 pillar_1.9.0 metapod_1.10.1 jsonlite_1.8.8 [213] GetoptLong_1.0.5
The text was updated successfully, but these errors were encountered:
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Describe the issue
filterMaf returns errors whenever I try to run it
Command
output:
Session info
Run
sessionInfo()
and post the output belowThe text was updated successfully, but these errors were encountered: