UNDO (version 1.14.0)

mixing_matrix_computation: Calculate and scale the mixing matrix

Description

Calculate the mixing matrix based on the output from marker_gene_selection(), and scale the mixing matrix to make the sum of proportions from tumor and stroma equal to 1. The pure expression levels of tumor and stroma are also computed.

Usage

mixing_matrix_computation(X, a1, a2, dimenMatrix)

Arguments

X

Gene expression data matrix

a1

The slope of marker genes in source 1

a2

The slope of marker genes in source 2

dimenMatrix

The dimention reduction matrix used to recover mixing matrix for all the samples

Value

Aest

estimated mixing matrix

Sest

estimated pure gene expression of two sources

Examples

a1<- matrix(runif(2),2,1)
a2<- matrix(runif(2),2,1)
X <- 1000*matrix(runif(20000),10000,2)
dimenMatrix <- NULL
Deconv <- mixing_matrix_computation(X, a1, a2, dimenMatrix)