Entering edit mode
I try to import merged maf files . I have this error:
R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Workspace loaded from ~/Desktop/.RData] > library(maftools) ds = read.maf(maf ="MERGE.data.maf", verbose = FALSE, isTCGA = F) reading maf.. Read 90524 rows and 1 (of 1) columns from 0.463 GB file in 00:00:14 Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Hugo_Symbol > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /home/maurizio/miniconda2/envs/MAFIA/lib/R/lib/libRblas.so LAPACK: /home/maurizio/miniconda2/envs/MAFIA/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=it_IT.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] maftools_1.4.21 Biobase_2.38.0 BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] httr_1.3.1 RMySQL_0.10.11 bit64_0.9-7 splines_3.4.1 [5] foreach_1.4.4 assertthat_0.2.0 stats4_3.4.1 blob_1.1.0 [9] BSgenome_1.46.0 GenomeInfoDbData_1.0.0 Rsamtools_1.30.0 slam_0.1-42 [13] progress_1.1.2 ggrepel_0.7.0 pillar_1.1.0 RSQLite_2.0 [17] lattice_0.20-35 digest_0.6.15 GenomicRanges_1.30.2 RColorBrewer_1.1-2 [21] XVector_0.18.0 colorspace_1.3-2 cowplot_0.9.2 Matrix_1.2-12 [25] plyr_1.8.4 XML_3.98-1.10 GetoptLong_0.1.6 biomaRt_2.34.2 [29] zlibbioc_1.24.0 xtable_1.8-2 scales_0.5.0 BiocParallel_1.12.0 [33] tibble_1.4.2 pkgmaker_0.22 IRanges_2.12.0 ggplot2_2.2.1 [37] SummarizedExperiment_1.8.0 GenomicFeatures_1.30.0 lazyeval_0.2.1 mclust_5.4 [41] survival_2.41-3 magrittr_1.5 memoise_1.1.0 doParallel_1.0.11 [45] changepoint_2.2.2 NMF_0.20.6 tools_3.4.1 registry_0.5 [49] data.table_1.10.4-3 prettyunits_1.0.2 GlobalOptions_0.0.12 matrixStats_0.52.2 [53] gridBase_0.4-7 ComplexHeatmap_1.17.1 stringr_1.3.0 S4Vectors_0.16.0 [57] munsell_0.4.3 cluster_2.0.6 rngtools_1.2.4 DelayedArray_0.4.1 [61] AnnotationDbi_1.40.0 Biostrings_2.46.0 compiler_3.4.1 GenomeInfoDb_1.14.0 [65] rlang_0.2.0 grid_3.4.1 RCurl_1.95-4.10 iterators_1.0.9 [69] VariantAnnotation_1.24.5 rjson_0.2.15 circlize_0.4.3 bitops_1.0-6 [73] gtable_0.2.0 codetools_0.2-15 DBI_0.7 reshape2_1.4.3 [77] R6_2.2.2 gridExtra_2.3 zoo_1.8-1 GenomicAlignments_1.14.0 [81] rtracklayer_1.38.0 bit_1.1-12 shape_1.4.4 stringi_1.1.6 [85] Rcpp_0.12.15 wordcloud_2.5