The INDEED R package provides important functions as shown below: non_partial_cor(), select_rho_partial(), partial_cor(), and network_display().
non_partial_cor function performs typical correlation analysis based on user input data, class label, p-value, sample id, number of permutations, and the method (default pearson) p value is optional, the result of score table and differential network will be returned
select_rho_partial function preprocesses data for partical correlation analysis, the result contains list of preprocessed data and rho values and error plot for user to choose desired rho value for graphical lasso
partial_cor function performs partical correlation analysis based on user input preprocessed list from select_rho_partial step and the rho choosing method or values of their choice and number of permutations (default 1000), p-value is optional, the result of score table and differential network will be returned
A function to assist in the network visualization of the result from INDEED functions non_partial_cor() and patial_cor().
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