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No non-synonymous mutations found Check vc_nonSyn argumet in read.maf` for details #838

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guohout opened this issue Jun 3, 2022 · 4 comments
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No non-synonymous mutations found Check vc_nonSyn argumet in read.maf` for details #838

guohout opened this issue Jun 3, 2022 · 4 comments
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@guohout
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guohout commented Jun 3, 2022 •
edited by PoisonAlien
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library(TCGAbiolinks) 
query_SNV <- GDCquery(project = "TCGA-LIHC", 
                      data.category = "Simple Nucleotide Variation", 
                      data.type = "Masked Somatic Mutation", 
                      workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking") 
GDCdownload(query_SNV) 
mafFilePath2 = dir(path = "GDCdata/TCGA-LIHC",pattern = "masked.maf.gz$",full.names = T,recursive=T) 
library(maftools)
mafdata2 <- lapply(mafFilePath2, function(x) {read.maf(x,isTCGA = T)}) 
snv_data2 = merge_mafs(mafdata2)

1654259683(1)
1654259768(1)
Why this error occurred, thank you for your answer.
@PoisonAlien
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Hi,
I couldn't figure out the issue. But try the below workaround..

library(TCGAbiolinks) 
query_SNV <- GDCquery(project = "TCGA-LIHC", 
                      data.category = "Simple Nucleotide Variation", 
                      data.type = "Masked Somatic Mutation", 
                      workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking") 
GDCdownload(query_SNV) 
mafFilePath2 = dir(path = "GDCdata/TCGA-LIHC",pattern = "masked.maf.gz$",full.names = T,recursive=T) 

library(maftools)
x = lapply(mafFilePath2, data.table::fread, skip = "Hugo_Symbol")
x = data.table::rbindlist(l = x, use.names = TRUE, fill = TRUE)
xm = maftools::read.maf(maf = x)

Hope this helps.

@li910493462
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i have the same error,please help me,thank you

@github-actions
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This issue is stale because it has been open for 60 days with no activity.

@github-actions github-actions bot added the stale label Aug 18, 2023
@github-actions
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github-actions bot commented Sep 1, 2023

This issue was closed because it has been inactive for 14 days since being marked as stale.

@github-actions github-actions bot closed this as completed Sep 1, 2023
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@PoisonAlien @guohout @li910493462