get_observed_synergies_per_cell_line

a character vector of the cell line directories, in the
form of {path}/cell_line_name. The cell line name directory
should be different for each element of the vector as we use it to fill in the
<code>rownames</code> of the result <code>data.frame</code> object. Inside each cell line directory
we read the observed synergies from a file called observed_synergies
(if it exists and is non-empty). This file has the names of the observed
drug combinations, one in each line.

cell.line.dirs

a character vector with elements the names of all the drug combinations
that were tested in the analysis.

drug.combos

Use this function to get the observed synergies from the respective
files inside the given list of cell line directories.

Analysis and visualization of an ensemble of boolean models for
biomarker discovery in cancer cell networks. The package allows to easily
import the data results of a software pipeline that predicts synergistic drug
combinations in cancer cell lines, developed by the DrugLogics research group
in NTNU. It has generic functions that can be used to split a boolean model
dataset to model groups with regards to the models predictive performance (number of true
positive predictions or Matthews correlation coefficient score) or synergy prediction based on a given set
of observed synergies and find the average activity difference per network
node between all group pairs. Thus, given user-specific thresholds,
important nodes (biomarkers) can be accessed in the sense that they make the
models predict specific synergies (synergy biomarkers) or have better
performance in general (performance biomarkers). Lastly, if the
boolean models have a specific equation form and differ only in their link operator,
link operator biomarkers can also be assessed.

get_observed_synergies_per_cell_line: Get observed synergies per cell line

Description

Usage

Arguments

Value