OncodriveFML
The simplest way to run OncodriveFML is through the Barcelona Biomedical Genomics (BBG) Lab website. If you haven’t already, sign up for an account on the website using the login button at the top right of the page.
After you’ve logged in, click on the Analysis tab at the top of the page.
Prior to running the analysis we need to do a bit of formatting on the MAF file.
Generating the Mutations file
The Mutations file is simply just a trimmed down version of the MAF.
oncodrive.input <- maf[ ,c("Chromosome",
"Start_position",
"Reference_Allele",
"Tumor_Seq_Allele2",
"Tumor_Sample_Barcode")]
names(oncodrive.input) <- c("CHROMOSOME",
"POSITION",
"REF",
"ALT",
"SAMPLE")
write.table(oncodrive.input, "~/Downloads/oncodrive_input.txt",
row.names = F, sep = '\t', quote = F)
Filling out the Analysis tab
Back in the Analysis tab, fill the inputs with the following:
Analysis title: TCGA_SKCM
Mutations file: upload ~/Downloads/oncodrive_input.txt here
Sequencing: Whole exome
Indels: Included
Genomic elements: Coding sequence
Leave the Advanced options inputs as the defaults.
Once all of the inputs are filled out, click the Submit button!