sample_test_1ctrl | R Documentation |
This function makes the test of the dysregulation of all genes for one patient. It's the adapted method for the datasets with only 1 control, if you want the normal Penda method used penda::sample_test
sample_test_1ctrl(sample, iterations, threshold)
sample |
A vector with all the genes expressions for one patient. |
iterations |
The maximal number of iterations for the test. If the dysregulation list no longer changes, iterations are stop before. |
threshold |
The threshold for regulation_test. |
This function return a list with two vectors : D, with TRUE for genes down-regulated U, with TRUE for genes up-regulated.
# First, load and define the data
dataset = penda::make_dataset_1ctrl(
penda::penda_data_ctrl[1:10, 1],
penda::penda_data_case[1:10, 1:3]
)
controls = dataset$data_ctrl
sample = dataset$data_case[,1]
# Second, lower and higher lists are computed
L_H_list = penda::compute_lower_and_higher_lists_1ctrl(controls, s_max = 50)
# Third, test is the expression is deregulated for each gene of a sample.
res_sample = penda::sample_test_1ctrl(sample,
iterations = 20,
threshold = 0.03)
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