mixing_matrix_computation {UNDO} | R Documentation

## 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

### Author(s)

Niya Wang (wangny@vt.edu)

### 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)

[Package UNDO version 1.29.0 Index]