bad fill option from read.maf()

[ShixiangWang]

When I use read.maf() function to read maf file from TCGA, Error occur

reading maf..
Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants,  : 
  missing required fields from MAF: Hugo_Symbol

So I debug this function and find fill option is bad for read maf file here.

> maf2 <- fread(maf, 
+               sep = "\t", stringsAsFactors = FALSE, verbose = FALSE, 
+               data.table = TRUE, showProgress = TRUE, header = TRUE, fill = TRUE)
> dim(maf2)
[1] 208185      1
> maf2 <- fread(maf, 
+               sep = "\t", stringsAsFactors = FALSE, verbose = FALSE, 
+               data.table = TRUE, showProgress = TRUE, header = TRUE, fill = FALSE)
|--------------------------------------------------|
|==================================================|
> dim(maf2)
[1] 208180    120

I don't know how fill change the result object, but indeed it generate this error.

[PoisonAlien]

Hi,

Can you post your sessioninfo ?

[ShixiangWang]

@PoisonAlien

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] bindrcpp_0.2.2      maftools_1.6.0      Biobase_2.40.0      BiocGenerics_0.26.0 data.table_1.11.0  
 [6] forcats_0.3.0       stringr_1.3.0       dplyr_0.7.4         purrr_0.2.4         readr_1.1.1        
[11] tidyr_0.8.0         tibble_1.4.2        ggplot2_2.2.1       tidyverse_1.2.1    

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            rjson_0.2.15                mclust_5.4                 
  [4] circlize_0.4.3              XVector_0.20.0              GenomicRanges_1.32.0       
  [7] GlobalOptions_0.0.13        rstudioapi_0.7              ggrepel_0.7.0              
 [10] bit64_0.9-7                 AnnotationDbi_1.42.0        lubridate_1.7.4            
 [13] xml2_1.2.0                  codetools_0.2-15            splines_3.5.0              
 [16] mnormt_1.5-5                doParallel_1.0.11           jsonlite_1.5               
 [19] Rsamtools_1.32.0            broom_0.4.4                 gridBase_0.4-7             
 [22] cluster_2.0.7-1             compiler_3.5.0              httr_1.3.1                 
 [25] assertthat_0.2.0            Matrix_1.2-14               lazyeval_0.2.1             
 [28] cli_1.0.0                   prettyunits_1.0.2           tools_3.5.0                
 [31] gtable_0.2.0                glue_1.2.0                  GenomeInfoDbData_1.1.0     
 [34] reshape2_1.4.3              Rcpp_0.12.16                slam_0.1-43                
 [37] cellranger_1.1.0            NMF_0.21.0                  Biostrings_2.48.0          
 [40] nlme_3.1-137                rtracklayer_1.40.0          iterators_1.0.9            
 [43] changepoint_2.2.2           psych_1.8.3.3               rvest_0.3.2                
 [46] devtools_1.13.5             rngtools_1.2.4              XML_3.98-1.11              
 [49] zlibbioc_1.26.0             zoo_1.8-1                   scales_0.5.0               
 [52] BSgenome_1.48.0             VariantAnnotation_1.26.0    hms_0.4.2                  
 [55] SummarizedExperiment_1.10.0 RColorBrewer_1.1-2          ComplexHeatmap_1.18.0      
 [58] yaml_2.1.19                 memoise_1.1.0               gridExtra_2.3              
 [61] pkgmaker_0.22               biomaRt_2.36.0              stringi_1.1.7              
 [64] RSQLite_2.1.0               S4Vectors_0.18.0            foreach_1.4.4              
 [67] GenomicFeatures_1.32.0      BiocParallel_1.13.1         shape_1.4.4                
 [70] GenomeInfoDb_1.16.0         rlang_0.2.0                 pkgconfig_2.0.1            
 [73] matrixStats_0.53.1          bitops_1.0-6                lattice_0.20-35            
 [76] bindr_0.1.1                 GenomicAlignments_1.16.0    tidyselect_0.2.4           
 [79] cowplot_0.9.2               bit_1.1-12                  plyr_1.8.4                 
 [82] magrittr_1.5                R6_2.2.2                    IRanges_2.14.0             
 [85] DelayedArray_0.6.0          DBI_1.0.0                   withr_2.1.2                
 [88] pillar_1.2.2                haven_1.1.1                 foreign_0.8-70             
 [91] survival_2.42-3             RCurl_1.95-4.10             modelr_0.1.1               
 [94] crayon_1.3.4                wordcloud_2.5               GetoptLong_0.1.6           
 [97] progress_1.1.2              grid_3.5.0                  readxl_1.1.0               
[100] blob_1.1.1                  digest_0.6.15               xtable_1.8-2               
[103] stats4_3.5.0                munsell_0.4.3               registry_0.5      

[PoisonAlien]

Does your file has header lines - starting with # ? Can you share your maf file, its hard for me to suggest without a reproducible example.

[ShixiangWang]

Yes, the data download from TCGA, it is very big, I put head 200 rows here and maybe you can test with it.

toy.txt

[PoisonAlien]

Hi, Just checked your file. 5th line of your maf file is incompatible with data.tables fread function. You can remove that particular line or all those header lines starting # and it should work fine. Let me know if this helps.

[ShixiangWang]

@PoisonAlien Thanks

[xinyueandtianliangle]

How did it happen? Can we remove 5th line of your maf file without opening it? Sorry, I met the same question. reading maf.. Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Hugo_Symbol

[PoisonAlien]

You could use sed command for it. If I remember correctly sed -5d would remove 5th line. But wait, could you double check your input file ? Can you share first 10 or 20 lines of your maf file ?