ISOpureS1.model_core.new_model

a GxD matrix representing gene expression profiles of tumor samples

tumordata

scalar strength parameter kappa placed over the reference cancer profile mm

kappa

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

INITIAL_VV

a (K-1)xG matrix, standardized so that all entries sum to 1, see 
		ISOpure.step1.CPE.R

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 1

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.

ISOpureS1.model_core.new_model: Initialize a model list to hold all the parameters

Description

Usage

Arguments

Value