results_simulation: Compare the results of the test on the simulation to the...

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

Compare the results of the test on the simulation to the reality.

Description

This function computes the number of false positive, true positive, false negative and false positive results after the test on a simulation.

Usage

results_simulation(D_matrix, U_matrix, simulation)

Arguments

D_matrix	The matrix of down-regulated genes.
U_matrix	The matrix of up-regulated genes.
simulation	The list of initial data $initial_data and modified data in $simulated_data

Value

This function returns a list of four integers : TP, the number of true postive results FP, the number of false postive results FN, the numbler of false negative results TN, the numbler of true negative results

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)
samples = simulation$simulated_data
# Second, lower and higher lists are computed
L_H_list = penda::compute_lower_and_higher_lists(controls, threshold = 0.99, s_max = 50)
# Third, test is the expression is deregulated for each gene of a sample
res_penda = penda::penda_test(samples,
                              controls,
                              iterations = 20,
                              L_H_list,
                              threshold = 0.03,
                              quant_test = 0,
                              factor_test = 1)
# Fourth, compare the result of the simulation to the reality
results = penda::results_simulation(res_penda$D,
                                    res_penda$U,
                                    simulation)

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