geneSelection.default {GSSTDA}

gene_selection_classes.default

Description

Private function to select Gene without DGSA process

Usage

## Default S3 method:
geneSelection(data_object, gen_select_type, percent_gen_select, na.rm = TRUE)

Arguments

data_object

Object with:

• full_data Input matrix whose columns correspond to the patients and rows to the genes.

• survival_time Numerical vector of the same length as the number of columns of full_data. Patients must be in the same order as in full_data. For the patients with tumour sample should be indicated the time between disease diagnosis and death (if not dead until the end of follow-up) and healthy patients must have an NA value.

• survival_event Numerical vector of the same length as the number of columns of full_data. Patients must be in the same order as in full_data. For the patients with tumour sample should be indicated whether the patient has died (1) or not (0). Only these values are valid and healthy patients must have an NA value.

• case_tag Character vector of the same length as the number of columns of full_data. Patients must be in the same order as in full_data. It must be indicated for each patient whether he/she is healthy or not. One value should be used to indicate whether the patient is healthy and another value should be used to indicate whether the patient's sample is tumourous. The user will then be asked which one indicates whether the patient is healthy. Only two values are valid in the vector in total.

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 geneSelection 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

data_object <- list("full_data" = full_data, "survival_time" = survival_time,
"survival_event" = survival_event, "case_tag" = case_tag)
class(data_object) <- "data_object"
geneSelection_object <- geneSelection(data_object, gen_select_type ="top_bot",
                                      percent_gen_select = 10)