marker_gene_selection: Select marker genes in two sources

In UNDO: Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

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

Author(s)

Niya Wang ([e-mail])

Examples

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

UNDO documentation built on Nov. 8, 2020, 7:53 p.m.