I want to know how to analyze TCGA data with maftools.
1
0
Entering edit mode
Y • 0
@3a4f472b
Last seen 20 months 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 • 1.1k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
Basti ▴ 750
@7d45153c
Last seen 1 hour 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"   
ADD COMMENT

Login before adding your answer.

Traffic: 853 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6