How can i download maf files form GDC Data Portal?
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@633250ec
Last seen 13 days ago
Poland

Hi, how can I download maf files from the GDC Data Portal? I downloaded files in gz format but can't open them in r.

maf_mutect2 <- GDCquery_Maf("COAD", pipelines = "mutect2") %>% subset(Sequencer == "Illumina HiSeq 2000") %>% read.maf
getGeneSummary(maf_mutect2)
genesummaries <- getGeneSummary(maf_mutect2)
getGeneSummary(maf_mutect2)
plotmafSummary(maf = maf_mutect2, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE)

'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


'data.table::fread(file = maf, sep = "\t", stringsAsFactors = FALSE, ':

maf R • 324 views
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