generate_disease_component: Generate disease component matrix.

In GSSTDA: Progression Analysis of Disease with Survival using Topological Data Analysis

Generate disease component matrix.

Description

This function produces a disease component matrix from an expression matrix and the denoised flattened matrix constructed from "healthy tissue data".

Usage

generate_disease_component(full_data, normal_space)

Arguments

full_data	Input matrix whose columns correspond to the patients and rows to the gens. Both tumour and healthy samples should be included.
normal_space	Denoised flattened matrix constructed from "healthy tissue data". Output of the function denoise_rectangular_matrix.

Value

Disease component matrix that contains the disease component of the provided normal space

Examples

full_data <- matrix(stats::rnorm(120),ncol=20)
normal_tissue <- t(full_data)
normal_tissue_f <- flatten_normal_tiss(normal_tissue)
normal_tissue_f_d <- denoise_rectangular_matrix(normal_tissue_f, gamma=NA)
disease_component <- generate_disease_component(t(full_data),normal_tissue_f_d)

GSSTDA documentation built on June 22, 2024, 10:44 a.m.