BEATAML1.0-COHORT MAF

Libraries

library(TCGAbiolinks)
Biobase::package.version("TCGAbiolinks")

[1] "2.31.2"

Query

query <- GDCquery(
  project = "BEATAML1.0-COHORT", 
  data.category = "Simple Nucleotide Variation", 
  access = "open",
  data.type = "Masked Somatic Mutation", 
  workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)

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o GDCquery: Searching in GDC database

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Genome of reference: hg38

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oo Accessing GDC. This might take a while...

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ooo Project: BEATAML1.0-COHORT

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oo Filtering results

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ooo By access

ooo By data.type

ooo By workflow.type

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oo Checking data

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ooo Checking if there are duplicated cases

ooo Checking if there are results for the query

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o Preparing output

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Download

GDCdownload(query)

Downloading data for project BEATAML1.0-COHORT

Of the 501 files for download 501 already exist.

All samples have been already downloaded

Prepare

maf <- GDCprepare(query)

dim(maf)

[1] 6148  140

head(maf)

# A tibble: 6 × 140
  Hugo_Symbol Entrez_Gene_Id Center         NCBI_Build Chromosome Start_Position
  <chr>                <int> <chr>          <chr>      <chr>               <int>
1 AHDC1                27245 OHSU Massivel… GRCh38     chr1             27548234
2 BEND5                79656 OHSU Massivel… GRCh38     chr1             48776862
3 STEAP3               55240 OHSU Massivel… GRCh38     chr2            119245709
4 KIAA2012         100652824 OHSU Massivel… GRCh38     chr2            202196883
5 ZBTB20               26137 OHSU Massivel… GRCh38     chr3            114350841
6 SRPK1                 6732 OHSU Massivel… GRCh38     chr6             35872579
# ℹ 134 more variables: End_Position <int>, Strand <chr>,
#   Variant_Classification <chr>, Variant_Type <chr>, Reference_Allele <chr>,
#   Tumor_Seq_Allele1 <chr>, Tumor_Seq_Allele2 <chr>, dbSNP_RS <chr>,
#   dbSNP_Val_Status <lgl>, Tumor_Sample_Barcode <chr>,
#   Matched_Norm_Sample_Barcode <chr>, Match_Norm_Seq_Allele1 <lgl>,
#   Match_Norm_Seq_Allele2 <lgl>, Tumor_Validation_Allele1 <lgl>,
#   Tumor_Validation_Allele2 <lgl>, Match_Norm_Validation_Allele1 <lgl>, …

Session information

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Sao_Paulo
tzcode source: internal

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

other attached packages:
[1] TCGAbiolinks_2.31.2

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0            dplyr_1.1.4                
 [3] blob_1.2.4                  filelock_1.0.2             
 [5] Biostrings_2.70.1           bitops_1.0-7               
 [7] fastmap_1.1.1               RCurl_1.98-1.13            
 [9] BiocFileCache_2.10.1        XML_3.99-0.15              
[11] digest_0.6.33               lifecycle_1.0.4            
[13] KEGGREST_1.42.0             RSQLite_2.3.3              
[15] magrittr_2.0.3              compiler_4.3.2             
[17] rlang_1.1.2                 progress_1.2.2             
[19] tools_4.3.2                 utf8_1.2.4                 
[21] yaml_2.3.8                  data.table_1.14.8          
[23] knitr_1.45                  prettyunits_1.2.0          
[25] S4Arrays_1.2.0              htmlwidgets_1.6.2          
[27] bit_4.0.5                   curl_5.1.0                 
[29] DelayedArray_0.28.0         plyr_1.8.9                 
[31] xml2_1.3.5                  abind_1.4-5                
[33] withr_2.5.2                 purrr_1.0.2                
[35] BiocGenerics_0.48.1         grid_4.3.2                 
[37] stats4_4.3.2                fansi_1.0.5                
[39] colorspace_2.1-0            ggplot2_3.4.4              
[41] scales_1.2.1                biomaRt_2.58.0             
[43] SummarizedExperiment_1.32.0 cli_3.6.1                  
[45] rmarkdown_2.25              crayon_1.5.2               
[47] generics_0.1.3              rstudioapi_0.15.0          
[49] httr_1.4.7                  tzdb_0.4.0                 
[51] DBI_1.1.3                   cachem_1.0.8               
[53] stringr_1.5.1               zlibbioc_1.48.0            
[55] parallel_4.3.2              rvest_1.0.3                
[57] AnnotationDbi_1.64.1        TCGAbiolinksGUI.data_1.22.0
[59] XVector_0.42.0              matrixStats_1.1.0          
[61] vctrs_0.6.4                 Matrix_1.6-1.1             
[63] jsonlite_1.8.7              IRanges_2.36.0             
[65] hms_1.1.3                   S4Vectors_0.40.1           
[67] bit64_4.0.5                 tidyr_1.3.0                
[69] glue_1.6.2                  stringi_1.8.2              
[71] gtable_0.3.4                GenomeInfoDb_1.38.1        
[73] GenomicRanges_1.54.1        munsell_0.5.0              
[75] tibble_3.2.1                pillar_1.9.0               
[77] rappdirs_0.3.3              htmltools_0.5.7            
[79] GenomeInfoDbData_1.2.11     R6_2.5.1                   
[81] dbplyr_2.4.0                vroom_1.6.4                
[83] evaluate_0.23               lattice_0.22-5             
[85] Biobase_2.62.0              readr_2.1.4                
[87] png_0.1-8                   memoise_2.0.1              
[89] Rcpp_1.0.11                 SparseArray_1.2.2          
[91] downloader_0.4              xfun_0.41                  
[93] MatrixGenerics_1.14.0       pkgconfig_2.0.3