I want to know how to analyze TCGA data with maftools.
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Y • 0
@3a4f472b
Last seen 9 weeks ago
Japan

Hi,

This is an example of reading TCGA-LAML data from maftools. Here is an example from "?maftools".

''' laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools')

laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools')

laml = read.maf(maf = laml.maf, clinicalData = laml.clin) '''

This example worked well.

I want to analyze melanoma data, so I changed

''' skcm.maf = system.file('extdata', 'tcga_skcm.maf.gz', package = 'maftools') '''

but it does not work well.

Please let me know if you know how to solve this problem.

sessioninfo

R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.3.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached): [1] fansi_1.0.3 digest_0.6.29 assertthat_0.2.1 utf8_1.2.2
[5] dplyr_1.0.9 R6_2.5.1 DBI_1.1.3 lifecycle_1.0.1
[9] magrittr_2.0.3 pillar_1.8.0 rlang_1.0.4 cli_3.3.0
[13] rstudioapi_0.13 DT_0.23 vctrs_0.4.1 generics_0.1.3
[17] ellipsis_0.3.2 tools_4.2.0 htmlwidgets_1.5.4 glue_1.6.2
[21] purrr_0.3.4 fastmap_1.1.0 compiler_4.2.0 pkgconfig_2.0.3
[25] htmltools_0.5.3 tidyselect_1.1.2 tibble_3.1.7

TCGAWorkflowData • 172 views
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You would have to get the appropriate data from a service such as the Genomic Data Commons Data Portal. https://portal.gdc.cancer.gov/

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Basti ▴ 440
@7d45153c
Last seen 6 minutes ago
France

There is no file called tcga_skcm.maf.gz inside maftools package :

list.files(system.file('extdata', package = 'maftools'))
 [1] "all_lesions.conf_99.txt"                           
 [2] "amp_genes.conf_99.txt"                             
 [3] "APL_primary.maf.gz"                                
 [4] "APL_relapse.maf.gz"                                
 [5] "BP_SMGs.txt.gz"                                    
 [6] "brca.maf.gz"                                       
 [7] "cancerhotspots_v2_GRCh37.tsv"                      
 [8] "cancerhotspots_v2_GRCh38.tsv"                      
 [9] "cancerhotspots_v2_hg19.tsv"                        
[10] "cancerhotspots_v2_hg38.tsv"                        
[11] "categories.tsv.gz"                                 
[12] "del_genes.conf_99.txt"                             
[13] "drugs.tsv.gz"                                      
[14] "ensGenes.txt.gz"                                   
[15] "hugo_to_mutSigSymbol.txt.gz"                       
[16] "LAML_sig_genes.txt.gz"                             
[17] "legacy_signatures.RDs"                             
[18] "oncogenic_sig_patwhays.tsv"                        
[19] "pancan.txt.gz"                                     
[20] "prot_len.txt.gz"                                   
[21] "protein_domains.RDs"                               
[22] "SBS_signatures.RDs"                                
[23] "scores.gistic"                                     
[24] "simple_somatic_mutation.open.ESCA-CN.sample.tsv.gz"
[25] "tcga_cohort.txt.gz"                                
[26] "tcga_laml_annot.tsv"                               
[27] "tcga_laml.maf.gz"                                  
[28] "TCGA.AB.3009.hg19.seg.txt"                         
[29] "variants.hg19_multianno.txt"                       
[30] "variants.tsv"   
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