Oncoplot with own MutSig file
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rina ▴ 30
@rina-16738
Last seen 14 months ago
France

Hi all,

I am trying to produce an oncoplot using the maftools package. I have performed a MutSig analysis myself and I would like to use the results in the plot. I have loaded the cms1siggenes in my R environment, but I get the following error. Any ideas how to solve for this?

> oncoplot(maf = maf.CMS1, top = 30, mutsig = cms1_sig_genes)
Error in data.table::fread(input = mutsig, sep = "\t", stringsAsFactors = FALSE,  : 
  input= must be a single character string containing a file name, a system command containing at least one space, a URL starting 'http[s]://', 'ftp[s]://' or 'file://', or, the input data itself containing at least one \n or \r

Thank you!

maftools mutsig • 1.2k views
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To anyone that might be facing the same problem, I managed to solve this by setting

> cms1_sig_genes <- "C:/User/path/to/sig.genes/file"
> oncoplot(maf = maf.CMS1, top = 30, mutsig = cms1_sig_genes)
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