function GDCquery_Maf error
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4 months ago
Negatyvna • 0

Hi, this is a completely fresh topic for me. I'm trying to do an analysis on the frequency of mutations in colorectal cancer. A week ago I used this function and it worked. Today I wanted to do a further analysis and I get this error. What can I do about this? Thanks for any help.

maf_mutect2 <- GDCquery_Maf("COAD", pipelines = "mutect2") 

Error: 'GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation", ': Please set a valid workflow.type argument from the list below: => Aliquot Ensemble Somatic Variant Merging and Masking
GDCquery_Maf R maftools • 717 views
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I have same problem, Did you find any solution? Kevin Blighe Can you please point what is the problem? My code is:

mut.maf <- GDCquery_Maf(tumor = "BRCA", pipelines = "somaticsniper")
============================================================================
 For more information about MAF data please read the following GDC manual and web pages:
 GDC manual: https://gdc-docs.nci.nih.gov/Data/PDF/Data_UG.pdf
 https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
 https://gdc.cancer.gov/about-gdc/variant-calling-gdc
============================================================================
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-BRCA
--------------------
oo Filtering results
--------------------
ooo By access
ooo By data.type
Error in GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation",  : 
  Please set a valid workflow.type argument from the list below:
  => Aliquot Ensemble Somatic Variant Merging and Masking
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ref: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/511

copy/pasted:

GDCquery_Maf was removed from the latest version of the package after GDC last update.
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ok, thanks cpad0112 for letting me know, it is helpful..

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