test_multiple_thresholds: Test gene expression variations for multiple thresholds

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

Test gene expression variations for multiple thresholds

Description

This function makes the Penda dysregulation test for different values of the threshold.

Usage

test_multiple_thresholds(simulation, threshold_values, iterations)

Arguments

simulation	The simulation with the list of initial data $initial_data and modified data in $simulated_data.
threshold_values	The vector of values of the threshold for the regulation test.
iterations	The maximal number of iterations for the test. If the dysregulation list no longer changes, iterations are stop before.

Value

This function returns a list of two logical matrices. The D matrix with for each threshold TRUE for genes down-regulated, and the U matrix with TRUE for genes up-regulated.

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[,13]
controls = controls[,-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.
#   When this function is called, quantiles are already computed
quant_test = 0
factor_test = 1
quantile_genes = apply(controls, 1, quantile, c(quant_test,(1-quant_test)), na.rm = TRUE)
quantile_genes[1,] = quantile_genes[1,] / factor_test
# quantile_genes[2,] = quantile_genes[2,] * factor_test
res_penda = penda::test_multiple_thresholds(simulation,
                                threshold_values,
                                iterations = 20)

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