How can i download maf files form GDC Data Portal?
0
0
Entering edit mode
@633250ec
Last seen 2.4 years 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 • 2.5k views
ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 520 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6