plotMutationSpectrum function,I want to know the exact process of calculating contribution.
Regarding second question I have run the same code 10 times,please have a look at the link for the code https://www.dropbox.com/s/sug1i8v1zoqm1ce/Mutation_signature_package_data.R?dl=0
Please have a look at this link https://www.dropbox.com/s/p30pdl0a7ifdv7a/ss1_ss2.png?dl=0 where I have attached an image of two plots which are slightly different to each other. I have used this function
plotSignatures(sigs_nmf) + ggtitle("Somatic Signatures: NMF - Barchart") and run this 10 times on the dataset supplied with the package,the plot on the right side occurred 8 times whereas the plot on the left side occurred 2 times.
We have also run this for our dataset but the dissimilarity is more.
Another question is that for your dataset supplied with the package,what is the index column meant for?
Also,what do to if I have to run this package for chr X,chr Y,chr MT.Is this package supports this?