Description Usage Arguments Value Examples
Plot the signature ratio
1 2 |
trTmMut |
Either a data frame or location of input text file, where rows are samples, columns are trinucleotide contexts. Use data(randomly.generated.tumors) to see the example data. |
tmSite |
Site of sample. |
country |
Country of sample. |
tmMutRef |
Location of the mutation file that is to be converted or name of data frame in environment. "tmMutRef" is the standard signature value for one site and one country. Default value is "mSigdb" that convert from "mSignatureDB" database. USe data("mSigdb") to see the example dasta. |
sampleId |
Name of sample. |
contexts.needed |
FALSE if tumor.file is a context file, TRUE if it is only mutation counts. |
tri.counts.method |
Set to either:
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Plot a histogram to compare sample and ref.
1 | testPlot = plotSig(trTmMut = sample.mut.trans, tmSite = "bone", country = "UK", sampleId = "1", contexts.needed = TRUE)
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