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PoisonAlien
filterMaf error
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
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
