This function builds a binary, incidence, matrix from the cnr$X. It was designed as a helper function to generate the input for infSCITE.
a copy number matrix to convert to an incidence matrix
Because infSCITE was developed for mutation data, this function creates a precense/absence matrix of the data
By default, anything not diploid is 1.
Returns an incidence matrix for X as part of the cnr object
Z incidence matrix from X, copy number != 2 is 1, all 2 are 0
1 2 3
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