PoisonAlien
commented
2 weeks ago Hi,
I am sorry for not getting back sooner.
It's just a message and nothing is ignored. You can set your preferred set of variant classifications as functional using the argument vcNonSyn in read.maf. I hope this helps.
I am a newbie in bioinformatics. When I use read.maf to read the file generated by annovartomaf, MNP is excluded. Why is MNP not considered?
sessionInfo() R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Asia/Shanghai tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] maftools_2.18.0 sigminer_2.3.0 arrow_16.1.0 Biobase_2.62.0 BiocGenerics_0.48.1
loaded via a namespace (and not attached): [1] splines_4.3.2 later_1.3.2 bitops_1.0-7
[4] ggplotify_0.1.2 filelock_1.0.3 tibble_3.2.1
[7] polyclip_1.10-6 fastDummies_1.7.3 lifecycle_1.0.4
[10] rstatix_0.7.2 doParallel_1.0.17 globals_0.16.2
[13] lattice_0.21-9 MASS_7.3-60 dendextend_1.17.1
[16] backports_1.4.1 magrittr_2.0.3 rmarkdown_2.25
[19] yaml_2.3.8 httpuv_1.6.13 NMF_0.30.1
[22] cowplot_1.1.2 DBI_1.2.2 RColorBrewer_1.1-3
[25] pkgload_1.3.3 abind_1.4-5 zlibbioc_1.48.0
[28] purrr_1.0.2 ggraph_2.1.0 RCurl_1.98-1.13
[31] yulab.utils_0.1.3 pkgmaker_0.32.10 tweenr_2.0.2
[34] rappdirs_0.3.3 circlize_0.4.15 GenomeInfoDbData_1.2.11
[37] IRanges_2.36.0 KMsurv_0.1-5 S4Vectors_0.40.2
[40] enrichplot_1.22.0 ggrepel_0.9.5 listenv_0.9.0
[43] tidytree_0.4.6 parallelly_1.36.0 codetools_0.2-19
[46] DOSE_3.28.2 DNAcopy_1.76.0 ggforce_0.4.1
[49] tidyselect_1.2.0 shape_1.4.6 aplot_0.2.2
[52] farver_2.1.1 viridis_0.6.4 matrixStats_1.2.0
[55] stats4_4.3.2 BiocFileCache_2.10.2 jsonlite_1.8.8
[58] GetoptLong_1.0.5 ellipsis_0.3.2 tidygraph_1.3.0
[61] survival_3.5-7 iterators_1.0.14 foreach_1.5.2
[64] tools_4.3.2 treeio_1.26.0 Rcpp_1.0.11
[67] glue_1.6.2 gridExtra_2.3 xfun_0.41
[70] qvalue_2.34.0 GenomeInfoDb_1.38.2 dplyr_1.1.4
[73] withr_2.5.2 BiocManager_1.30.22 fastmap_1.1.1
[76] fansi_1.0.6 digest_0.6.33 mime_0.12
[79] R6_2.5.1 gridGraphics_0.5-1 colorspace_2.1-0
[82] GO.db_3.18.0 RSQLite_2.3.6 utf8_1.2.4
[85] tidyr_1.3.0 generics_0.1.3 data.table_1.14.10
[88] graphlayouts_1.0.2 httr_1.4.7 scatterpie_0.2.1
[91] pkgconfig_2.0.3 gtable_0.3.4 blob_1.2.4
[94] registry_0.5-1 ComplexHeatmap_2.18.0 XVector_0.42.0
[97] furrr_0.3.1 survMisc_0.5.6 clusterProfiler_4.10.0
[100] shadowtext_0.1.2 htmltools_0.5.7 carData_3.0-5
[103] fgsea_1.28.0 clue_0.3-65 scales_1.3.0
[106] png_0.1-8 ggfun_0.1.3 knitr_1.45
[109] km.ci_0.5-6 rstudioapi_0.15.0 tzdb_0.4.0
[112] reshape2_1.4.4 rjson_0.2.21 nlme_3.1-164
[115] curl_5.2.0 cachem_1.0.8 zoo_1.8-12
[118] GlobalOptions_0.1.2 stringr_1.5.1 BiocVersion_3.18.1
[121] parallel_4.3.2 HDO.db_0.99.1 AnnotationDbi_1.64.1
[124] pillar_1.9.0 grid_4.3.2 vctrs_0.6.5
[127] promises_1.2.1 ggpubr_0.6.0 car_3.1-2
[130] dbplyr_2.4.0 xtable_1.8-4 cluster_2.1.6
[133] evaluate_0.23 cli_3.6.2 compiler_4.3.2
[136] rlang_1.1.2 crayon_1.5.2 rngtools_1.5.2
[139] ggsignif_0.6.4 survminer_0.4.9 plyr_1.8.9
[142] fs_1.6.3 stringi_1.8.3 viridisLite_0.4.2
[145] gridBase_0.4-7 BiocParallel_1.36.0 assertthat_0.2.1
[148] munsell_0.5.0 Biostrings_2.70.1 lazyeval_0.2.2
[151] GOSemSim_2.28.0 Matrix_1.6-1.1 patchwork_1.2.0
[154] future_1.33.1 bit64_4.0.5 ggplot2_3.4.4
[157] KEGGREST_1.42.0 shiny_1.8.0 interactiveDisplayBase_1.40.0 [160] AnnotationHub_3.10.1 igraph_1.6.0 broom_1.0.5
[163] memoise_2.0.1 ggtree_3.10.0 fastmatch_1.1-4
[166] bit_4.0.5 ape_5.7-1 gson_0.1.0