gene_selection_surv {GSSTDA} | R Documentation |
Gene selection based on variability and the relationship to survival.
Description
It selects genes for mapper based on the product of standard deviation of the rows (genes) in the disease component matrix plus one times the Z score obtained by fitting a cox proportional hazard model to the level of each gene. For further information see "Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival"
Usage
gene_selection_surv(
case_disease_component,
cox_all_matrix,
gen_select_type,
num_gen_select
)
Arguments
case_disease_component |
Disease component matrix (output of the function
|
cox_all_matrix |
Output from the |
gen_select_type |
Option. 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). |
num_gen_select |
Number of genes to be selected (those with the highest product value). |
Value
Character vector with the names of the selected genes.