gene_selection_ {GSSTDA}

Private gene_selection_

Description

Private function to gene selection

Usage

gene_selection_(
  full_data,
  survival_time,
  survival_event,
  control_tag_cases,
  gen_select_type,
  num_gen_select,
  matrix_disease_component = NULL
)

Arguments

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. In addition, the patients must be in the same order as in full_data. For the patients whose sample is pathological should be indicated the time between the disease diagnosis and event (death, relapse or other). If the event has not occurred, it should be indicated the time until the end of follow-up. Patients whose sample is from healthy tissue 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 the patients with pathological sample should be indicated whether the event has occurred (1) or not (0). Only these values are valid and healthy patients must have an NA value.

control_tag_cases

Numeric vector with the indices of the columns corresponding to the healthy sample patients.

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.

num_gen_select

Number of genes to be selected to be used in mapper.

matrix_disease_component

Optional, only necessary in case of gene selection after dsga has been performed. Matrix of the disease components (the transformed full_data matrix from which the normal component has been removed) from the dsga_function.

Value

A gene_selection_object. It contains:

• the matrix with which the gene selection has been performed without NAN's values (data). It is the matrix_disease_component in case it has been performed from a dsga_object or full_data in the opposite case.

• the cox_all_matrix (a matrix with the results of the application of proportional hazard models: with the regression coefficients, the odds ratios, the standard errors of each coefficient, the Z values (coef/se_coef) and the p-values for each Z value)

• a vector with the name of the selected genes

• the matrix of disease components with only the rows of the selected genes (genes_disease_component)

• and the vector of the values of the filter function.

Examples

gen_select_type <- "Top_Bot"
percent_gen_select <- 10
control_tag_cases <- which(case_tag == "NT")
gene_selection_obj <- gene_selection_(full_data, survival_time, survival_event,
control_tag_cases, gen_select_type ="top_bot", num_gen_select = 10)