Closed hylkedonker closed 2 years ago
Hi Hylke,
The signatures are W and the activities of those signatures are H (Unless you have some transpose on mutation spectrum X.) In our Sigprofiler tools the mutational matrix or what you call a spectrum, X, has dimensions m x n i.e. context type x samples. Our signatures are W (context_type x number_of_signatures k) and H are activities (number_of_signatures k x Samples).
Please try again by using accurate Signatures and Activities and reopen the ticket if the issue persists.
Ravi.
Hi,
I have a mutation spectrum
X
and given COSMIC's mutational signatureH
I want to computeW
so thatX=WH
. In otherwords, I want to computeW=X H^{-1}
. If I understand it correctly, this should be the purpose of this package, right?I conducted a small experiment to see if everything works as I expected. I choose some
W
to check if SigProfilerAssignment can correctly reconstruct itand check if
W_true
is close toW_reconstr
. Unfortunately, it is not even close. Probably I misinterpreted something of the program, e.g., what files to use (I assumedAssignment_Solution_Activities.txt
containsW_reconstr
). Could you help me out to pinpoint what went wrong?Here is a minimal example that reproduces my problem:
Thanks in advance,
Hylke