UNDO (version 1.14.0)

marker_gene_selection: Select marker genes in two sources

Description

Select the marker genes in tumor and stroma in an unsupervised way

Usage

marker_gene_selection(X, lowper, highper, epsilon1, epsilon2)

Arguments

X

gene expression data

lowper

The percentage of genes the user wants to remove with lowest norm. The range should be between 0 and 1.

highper

The percentage of genes the user wants to remove with highest norm.The range should be between 0 and 1.

epsilon1

Influence the number of marker genes. With increasing of epsilon1, the number marker genes in source 1 will increase. The value should be positive.

epsilon2

Influence the number of marker genes. With increasing of epsilon1, the number marker genes in source 2 will increase. The value should be positive.

Value

a1

The slope of marker genes in source 1

a2

The slope of marker genes in source 2

MG1

The gene list of marker genes in source 1

MG2

The gene list of marker genes in source 2

dimenMatrix

dimension reduction matrix

Examples

X <- matrix(runif(20000),10000,2)
MG_set <- marker_gene_selection(X, 0.4, 0.1, 0.1, 0.1)