get_perf_biomarkers_per_cell_line

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
<code>rownames</code> of the result <code>data.frame</code> object. Inside each {dir}
(the directory name does not matter, but 'biomarkers' is a good choice),
we read the biomarkers from two files (if they exist and are non-empty):
biomarkers_active and biomarkers_inhibited, which have the
active and inhibited performance biomarkers for each cell line (these files
have a list of node names/biomarkers, one in each line).

biomarkers.dirs

a character vector of the node names used in the analysis.
The biomarker names taken from the files inside the given directories must be
a subset of this vector.

node.names

Use this function to get the performance biomarkers from the respective
files inside the given list of 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_perf_biomarkers_per_cell_line: Get performance biomarkers per cell line

Description

Usage

Arguments

Value