get_synergy_biomarkers_from_dir

a character vector of the synergies (drug
combination names) that were predicted by at least one of the models
in the dataset.

predicted.synergies

string. It specifies the full path name of the
directory which holds the biomarker files. The biomarker files must be
formatted as: %drug.comb%_biomarkers_active or
%drug.comb%_biomarkers_inhibited, where %drug.comb% is an element
of the <code>predicted.synergies</code> vector.

biomarkers.dir

string. A directory with .gitsbe files/models. It's
needed in order to call <code><a rd-options="" href="/link/get_node_names?package=emba&version=0.1.1" data-mini-rdoc="emba::get_node_names">get_node_names</a></code>.

models.dir

a character vector which has the names of the nodes. If it's
not NULL, then it will be used instead of the <code>models.dir</code> parameter.
The <code>node.names</code> should include all the nodes that are reported as
biomarkers in the biomarker files inside the <code>biomarkers.dir</code> directory.
Default value: NULL.

node.names

This function reads the synergy biomarker files inside the given directory and merges
the results into a <code>data.frame</code> which it returns. This functions should
be used when the synergy biomarker results are in separate files inside the
directory given (see <code>biomarkers.dir</code> parameter).

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.

John Zobolas

emba

Ensemble Boolean Model Biomarker Analysis

get_synergy_biomarkers_from_dir function

string. A directory with .gitsbe files/models. It's
needed in order to call <code><a rd-options='' href='get_node_names'>get_node_names</a></code>.

get_synergy_biomarkers_from_dir: Get synergy biomarkers from dir

Description

Usage

Arguments

Value