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

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No non-synonymous mutations found Check vc_nonSyn argumet in read.maf` for details#838
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@guohout
guohout
opened on Jun 3, 2022 · edited by PoisonAlien
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.

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PoisonAlien

PoisonAlien commented on Jun 4, 2022

@PoisonAlien
PoisonAlien
on Jun 4, 2022
Owner

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

li910493462 commented on Sep 20, 2022

@li910493462
li910493462
on Sep 20, 2022

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

github-actions

github-actions commented on Aug 18, 2023

@github-actions
github-actionsbot
on Aug 18, 2023

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

github-actions
added
stale
on Aug 18, 2023
github-actions

github-actions commented on Sep 1, 2023

@github-actions
github-actionsbot
on Sep 1, 2023

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

github-actions
closed this as completedon Sep 1, 2023
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          No non-synonymous mutations found Check `vc_nonSyn`` argumet in `read.maf` for details · Issue #838 · PoisonAlien/maftools