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cannot read maf #14

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xiaodingliu opened this issue Feb 10, 2023 · 0 comments
Open

cannot read maf #14

xiaodingliu opened this issue Feb 10, 2023 · 0 comments

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@xiaodingliu
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Hi!
After loading the study
How could I use them in maftool by reading maf?

tcga_load("luad")
Loading LUAD. Please cite: https://doi.org/10.1016/j.cels.2018.03.002 for reference
An object of class MAF
ID summary Mean Median
1: NCBI_Build NA NA NA
2: Center NA NA NA
3: Samples 517 NA NA
4: nGenes 17130 NA NA
5: Frame_Shift_Del 4021 7.778 5
6: Frame_Shift_Ins 1185 2.292 1
7: In_Frame_Del 388 0.750 0
8: In_Frame_Ins 37 0.072 0
9: Missense_Mutation 133671 258.551 177
10: Nonsense_Mutation 11074 21.420 13
11: Nonstop_Mutation 179 0.346 0
12: Splice_Site 4469 8.644 5
13: Translation_Start_Site 225 0.435 0
14: total 155249 300.288 202

I tired...

maftools::read.maf(rbind(tcga_luad@data))
Error in rbind(tcga_luad@data) : object 'tcga_luad' not found

or

luad = read.maf(maf = 'inst/extdata/MC3/luad.RDs')
-Reading
Error in data.table::fread(file = maf, sep = "\t", stringsAsFactors = FALSE, :
File 'inst/extdata/MC3/luad.RDs' does not exist or is non-readable. getwd()=='/Users/dingdingdingplus'

Thank you very much!

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