This function uses the get_avg_activity_diff_mat_based_on_specific_synergy_prediction
function with the parameter models.link.operator as input in the place of
models.stable.state, since the two matrices representing the two inputs
have the same data format (rows represent models, columns represent nodes,
and each value is a number in the [0,1] interval).
get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction(model.predictions,
models.link.operator, predicted.synergies)a data.frame object with rows the models and
columns the drug combinations. Possible values for each model-drug combination
element are either 0 (no synergy predicted), 1 (synergy was
predicted) or NA (couldn't find stable states in either the drug
combination inhibited model or in any of the two single-drug inhibited models)
matrix (nxm) with n models and m nodes. The row
names of the matrix specify the models' names (same order as in the
models.mcc parameter) whereas the column names specify the name of the
network nodes (gene, proteins, etc.). Possible values for each model-node
element are either 0 (AND NOT link operator), 1
(OR NOT link operator) or 0.5 if the node is not targeted by
both activating and inhibiting regulators (no link operator).
a character vector of the synergies (drug
combination names) that were predicted by at least one of the models
in the dataset. It must be a subset of the column names (the drug combinations)
of the model.predictions object.
a matrix whose rows are vectors of average node link operator differences between two groups of models where the classification for each individual row was based on the prediction or not of a specific synergistic drug combination. The row names are the predicted synergies, one per row, while the columns represent the network's node names. Values are in the [-1,1] interval. the classification was based on the models' MCC values.
So, if a node has a value close to -1 it means that on average, this node's boolean equation has the AND NOT link operator in the models that predicted the specified synergy while a value closer to 1 means that the node's boolean equation has mostly the OR NOT link operator in these models. A value closer to 0 indicates that the link operator in the node's boolean equation is not so much different between the models that predicted the synergy and those that did not and so it won't not be a node of interest when searching for synergy biomarkers - nodes whose parameterization (value of the link operator) affects the manifestation of synergy. A value exactly equal to 0 can also mean that this node didn't not have a link operator in its boolean equation (making it thus a non-important node with regard to the parameterization).
Other average data difference functions: get_avg_activity_diff_based_on_mcc_clustering,
get_avg_activity_diff_based_on_specific_synergy_prediction,
get_avg_activity_diff_based_on_synergy_set_cmp,
get_avg_activity_diff_based_on_tp_predictions,
get_avg_activity_diff_mat_based_on_mcc_clustering,
get_avg_activity_diff_mat_based_on_specific_synergy_prediction,
get_avg_activity_diff_mat_based_on_tp_predictions,
get_avg_link_operator_diff_mat_based_on_mcc_clustering,
get_avg_link_operator_diff_mat_based_on_tp_predictions