Question: Maftotols importer error
0
gravatar for jarod_v6@libero.it
16 months ago by
Italy
jarod_v6@libero.it40 wrote:

I try to import merged maf files . I have this error:

 

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[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
maftols • 206 views
ADD COMMENTlink written 16 months ago by jarod_v6@libero.it40
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