This function gets the (previously-found or 'old') synergy biomarkers from their
respective files and if any of these files are empty (no 'old' biomarkers
found) or non-existent, the 'new' biomarkers (given as input vector parameters) are
automatically saved. When the 'new' biomarkers share common nodes
with the 'old' biomarkers, there exist 3
possible ways to combine the results, given by the method parameter.
If no common nodes exist, no matter the method selected,
the 'new' biomarkers are added to the 'old' ones.
update_biomarker_files(biomarkers.dir, drug.comb, biomarkers.active.new,
biomarkers.inhibited.new, method = "replace")string. It specifies the full path name of the
directory which holds the biomarker files for the synergistic drug combination
specified in the parameter drug.comb. The biomarker files must be
formatted as: %drug.comb%_biomarkers_active or
%drug.comb%_biomarkers_inhibited, where %drug.comb% is the value
of the drug.comb parameter.
string. The drug combination (e.g. "A-B") that will be used to identify the related biomarker files.
a numeric vector whose names attribute includes the node names of the (newly found) active biomarkers for the specified synergy. The values of the vector are the average activity difference of each node, derived from a comparison between 2 different groups of models.
a numeric vector whose names attribute includes the node names of the (newly found) inhibited biomarkers for the specified synergy. The values of the vector are the average activity difference of each node, derived from a comparison between 2 different groups of models.
string. It specifies the method to use to update the biomarker files when there are common nodes between the 'old' and 'new' biomarkers:
replace(DEFAULT): we discard the 'old' biomarkers and keep
only the 'new' ones
prune.to.common: we keep only the common biomarkers
extend: we add to the 'old' set of biomarkers the extra ones
from the 'new' set that are not non-common to the 'old' ones, extending
thus the 'old' biomarker set