ISOpureR1.1.3 package

Perform calculation for Tumour Adjacent Cell (TAC) profiles

Minimize a differentiable multivariate function

Compute the derivative of the loglikelihood relevant to vv for step 1

Compute the loglikelihood relevant to vv for step 1

Perform first step of ISOpure purification algorithm

Perform second step of ISOpure purification algorithm

Log-sum-exp

Greater than operator

Less than operator

Modified logarithm function

Tiles matrix horizontally or vertically

Compute loglikelihood given all model parameters for step 1

Initialize a model list to hold all the parameters

Optimizes the ISOpure parameters for step 1

Compute loglikelihood relevant to kappa for step 1

Compute derivative of loglikelihood with respect to kappa for step 1

Compute loglikelihood relevant to kappa for step 1

Compute the derivative of the loglikelihood relevant to mm for step 1

Compute the loglikelihood relevant to mm for step 1

Compute loglikelihood relevant to omega for step 1

Compute the derivative of loglikelihood relevant to omega for step 1

Compute the loglikelihood relevant to omega for step 1

Optimize kappa in step 1

Optimize the reference cancer profile, m, in step 1

Optimize omega in step 1

Optimize theta in step 1

Optimize vv in step 1

Compute the derivative of loglikelihood relevant to theta for step 1

Compute the loglikelihood relevant to theta for step 1

Compute loglikelihood relevant to vv for step 1

Compute loglikelihood given all model parameters for step 2

Compute loglikelihood given all model parameters for step 2

Optimizes the ISOpure parameters for step 2

Compute the derivative of loglikelihood relevant to the patient cancer...

Compute the loglikelihood relevant to the patient cancer profiles, cc,...

Compute loglikelihood relevant to kappa for step 2

Compute derivative of loglikelihood with respect to kappa for step 2

Compute loglikelihood relevant to kappa for step 2

Optimize the tumor-specific cancer profiles in step 2

Optimize kappa in step 2

Optimize theta in step 2

Optimize vv in step 2

Compute the derivative of loglikelihood relevant to theta for step 2

Compute the loglikelihood relevant to theta for step 2

Compute loglikelihood relevant to vv for step 2