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 • 718 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")
============================================================================
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/
============================================================================
--------------------------------------
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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copy/pasted:

GDCquery_Maf was removed from the latest version of the package after GDC last update.

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