Use this function to get the synergy biomarkers for each cell line. The biomarkers must be stored in a single file inside each given cell line-specific directory.
get_synergy_biomarkers_per_cell_line(biomarkers.dirs)a character vector of the biomarker directories, in the
form of {path}/cell_line_name/{dir}. The cell line name directory
should be different for each element of the vector as we use it to fill in the
rownames of each cell line-specific data.frame object.
Inside each {dir}, we read the synergy biomarkers from a file (if it
exists and is non-empty) with the name biomarkers_per_synergy. This file
has as first row the node names (columns) while every next row starts with the row name
(drug combination name) followed by a series of numbers from the ternary set
{1,-1,0}, denoting thus which nodes where found as active biomarkers for that
synergy, inhibited or not at all as biomarkers.
a list of cell line-specific data frames (each element
from the list takes its name from the respective cell line).
Each cell-line specific data.frame object has as rows the
true positive predicted synergies for that particular cell line
and columns the network nodes (should be the same for all cell lines).
Possible values for each synergy-node
element in each cell line-specific data.frame are either 1
(active state biomarker), -1
(inhibited state biomarker) or 0 (not a biomarker).