R/diff.R
get_avg_link_operator_diff_based_on_synergy_set_cmp.Rd
This function uses the get_avg_activity_diff_based_on_synergy_set_cmp
which splits the models to 'good' and 'bad' based on the predictions
of two different synergy sets, one of them being a subset of the other.
The 'good' models are those that predict the synergy.set.str
(e.g. "A-B,A-C,B-C") while the 'bad' models are those that predict the
synergy.subset.str
(e.g. "A-B,B-C"). Then, for each network node,
the function finds the node's average link operator value in each of the two classes
(a value in the [0,1] interval, 0 being AND NOT and 1 being OR NOT)
and then subtracts the bad class average link operator value from the good one,
taking into account the given penalty
factor and the number of models
in the 'good' and 'bad' class respectively.
get_avg_link_operator_diff_based_on_synergy_set_cmp( synergy.set.str, synergy.subset.str, model.predictions, models.link.operator, penalty = 0 )
synergy.set.str | a string of drug combinations, comma-separated. The
number of the specified combinations must be larger than the ones defined
in the |
---|---|
synergy.subset.str | a string of drug combinations, comma-separated.
There must be at least one combination defined and all of them should also
be included in the |
model.predictions | a |
models.link.operator | a |
penalty | value between 0 and 1 (inclusive). A value of 0 means no penalty and a value of 1 is the strickest possible penalty. Default value is 0. This penalty is used as part of a weighted term to the difference in a value of interest (e.g. activity or link operator difference) between two group of models, to account for the difference in the number of models from each respective model group. |
a numeric vector with values in the [-1,1] interval (minimum and maximum possible average difference) and with the names attribute representing the name of the nodes.
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 extra synergy(-ies) that are included in the
synergy.set.str
but not in the synergy.subset.str
, whereas a
value closer to 1 means that the node's boolean equation has mostly the
OR NOT link operator in these models.
These nodes are potential link operator biomarkers because the
structure of their respective boolean equations (denoted by their link operator)
can influence the prediction performance of a model and make it predict the
extra synergy(-ies). 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 set and those that predicted it's subset,
so it won't not be a node of interest when searching for potential link operator
biomarkers for the extra synergy(-ies).
A value exactly equal to 0 can also mean that this node didn't not have a link operator
in its boolean equation, again making it a non-important indicator of difference
in model performance.
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_specific_synergy_prediction()
,
get_avg_link_operator_diff_mat_based_on_tp_predictions()