select_threshold_param: Select the better threshold to reach a given FDR.

In CDecamps/penda: A R package that performs personalized differential analysis of comics data

Select the better threshold to reach a given FDR.

Description

This function use the result of choose_threshold to give the parameter which allows to reach the given FDR. If there are multiple patients, it uses the median

Usage

select_threshold_param(which_threshold, FDR_max = 0.05)

Arguments

which_threshold	The matrix result of choose_threshold, with patient, FDR and threshold.
FDR_max	The maximum FDR wanted.

Value

This function returns a list of 2 parameters : the best threshold and the associated FDR.

Examples

# First, load and define the data, make the simulation
controls = penda::penda_data_ctrl[1:10, 1:13]
median_gene = apply(controls, 1, median, na.rm = TRUE)
median_gene = sort(median_gene)
controls = controls[names(median_gene), ]
simu_data = controls[,11:13]
controls = controls[,-(11:13)]
simulation = penda::simplified_simulation(simu_data, proportion = 0.3, threshold = 60)
# Second, lower and higher lists are computed
L_H_list = penda::compute_lower_and_higher_lists(controls, threshold = 0.99, s_max = 50)
# Third, choose the vector of threshold to test
threshold_values = c(0.1, 0.2, 0.3, 0.4, 0.5)
# Fourth, make the test on simulation for different thresholds
which_threshold = penda::choose_threshold(controls,
                                          L_H_list,
                                          iterations = 20,
                                          simulation,
                                          threshold_values,
                                          quant_test = 0,
                                          factor_test = 1)
# Fifth, use the function to automatically choose the better threshold
best_threshold = penda::select_threshold_param(which_threshold, FDR_max = 0.05)

CDecamps/penda documentation built on March 29, 2024, 3:26 a.m.