function GDCquery_Maf error
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@633250ec
Last seen 2.1 years ago
Poland

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") %>% subset(Sequencer == "Illumina HiSeq 2000") %>% read.maf

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

rstudio maftools • 1.2k views
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