ISOpureS2.model_core.new_model

a GxD matrix representing gene expression profiles of tumor samples

tumordata

a 1xD matrix which represents strength parameter kappa over cc, given the reference 
		profile mm

kappa

a vector with K components, the prior over mixing proportions, theta, with last 
		entry weighed more heavily

INITIAL_VV

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 

PPtranspose

a (K-1)xG matrix of the standardized normal profiles, so that they sum to 1

BBtranspose

Produces a list (the model) which initializes the parameters vv, log_BBtranspose, 
	PPtranspose, kappa, theta, omega, log_all_rates for step 2

math

Deconvolution of mixed tumour profiles into normal and cancer for each patient, using
the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires
mixed tumour profiles and a set of unmatched "basis" normal profiles.

ISOpureS2.model_core.new_model: Compute loglikelihood given all model parameters for step 2

Description

Usage

Arguments

Value