gene_selection.dsga_object: gene_selection_classes.dsga_object

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

gene_selection_classes.dsga_object

Description

Private function to select Gene with dsga object

Usage

## S3 method for class 'dsga_object'
gene_selection(data_object, gen_select_type, percent_gen_select, na.rm = TRUE)

Arguments

data_object	dsga object information
gen_select_type	Option. Options on how to select the genes to be used in the mapper. Select the "Abs" option, which means that the genes with the highest absolute value are chosen, or the "Top_Bot" option, which means that half of the selected genes are those with the highest value (positive value, i.e. worst survival prognosis) and the other half are those with the lowest value (negative value, i.e. best prognosis). "Top_Bot" default option.
percent_gen_select	Percentage (from zero to one hundred) of genes to be selected to be used in mapper. 10 default option.
na.rm	logical. If TRUE, NA rows are omitted. If FALSE, an error occurs in case of NA rows. TRUE default option.

Value

A gene_selection object. It contains: the full_data without NAN's values, the control tag of the healthy patient, the matrix with the normal space and the matrix of the disease components.

Examples

dsga_obj <- dsga(full_data, survival_time, survival_event, case_tag, na.rm = "checked")

gene_selection_object <- gene_selection(dsga_obj, gen_select_type ="top_bot",
                                      percent_gen_select = 10)

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