penda_test_1ctrl: Test gene expression variations in a serie of samples

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

Test gene expression variations in a serie of samples

Description

This function applies the function sample_test_1ctrl to a serie of samples. It's a special version of the Penda method for the datasets with only 1 control, if you want the normal Penda method used penda::penda_test

Usage

penda_test_1ctrl(samples, iterations, L_H_list, threshold)

Arguments

samples	A vector or a matrix with all the genes expressions for each sample.
iterations	The maximal number of iterations for the test. If the dysregulation list no longer changes, iterations are stop before.
L_H_list	The list of lower and higher expressed genes matrices in the control.
threshold	If Ll/Lh and Hh/Hl are under this threshold, the expression not change.

Value

This function return a list of two matrices (down_genes and up_genes)

Examples

# First, load and define the data
control = penda::penda_data_ctrl[1:10, 1]
samples = penda::penda_data_case[1:10, 1:3]
# Second, lower and higher lists are computed
L_H_list = penda::compute_lower_and_higher_lists_1ctrl(control, s_max = 50)
# Third, test is the expression is deregulated for each gene of a sample
res_penda = penda::penda_test_1ctrl(samples,
                              iterations = 20,
                              L_H_list = L_H_list,
                              threshold = 0.03)

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