Description Usage Arguments Value Author(s)
Produces a list (the model) which initializes the parameters vv, log_BBtranspose, PPtranspose, kappa, theta, omega, log_all_rates for step 2
1 | ISOpureS2.model_core.new_model(tumordata, kappa, INITIAL_VV, PPtranspose, BBtranspose)
|
tumordata |
a GxD matrix representing gene expression profiles of tumor samples |
kappa |
a 1xD matrix which represents strength parameter kappa over cc, given the reference profile mm |
INITIAL_VV |
a vector with K components, the prior over mixing proportions, theta, with last entry weighed more heavily |
PPtranspose |
the prior on the tumor-specific cancer profiles is just the reference cancer profile (1xG matrix) learned in ISOpureS1, standardized so that all entries sum to 1 |
BBtranspose |
a (K-1)xG matrix of the standardized normal profiles, so that they sum to 1 |
model |
a newly generated model list to hold all the parameters |
Gerald Quon, Catalina Anghel, Francis Nguyen
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