get_synergy_scores: Get synergy scores from file

In emba: Ensemble Boolean Model Biomarker Analysis

Description

Use this function to read Drabme's output files that have synergy scores for a list of tested drug perturbations.

Usage

get_synergy_scores(file_name, file_type = "ensemblewise")

Arguments

file_name	string. The name of the file, can be a full path.
file_type	string. The type of input file, can be either ensemblewise (default option) or modelwise.

Details

Two types of files can be read: the model-wise and the ensemble-wise synergies:

• The model-wise synergies data is structured as a 3-column table, first being the names of the tested drug combinations, second the number of models that predicted that combination as synergistic and the third the number of models that predicted the drug combination as non-synergistic.

• The ensemble-wise synergies data is structured as a 2-column table, the first being the names of drug combinations and the second the ensemble-wise synergy scores for those perturbations.

Note that no matter the file type, the first line of the file is always skipped and the columns must be tab-separated. See example below for the format of such files generated by the Drabme module.

Value

a tibble containing a representation of the data in the file.

Examples

ensemblewise_synergies_file = system.file("extdata", "ensemblewise_synergies",
  package = "emba", mustWork = TRUE)
modelwise_synergies_file = system.file("extdata", "modelwise_synergies",
  package = "emba", mustWork = TRUE)
data_ensemble = get_synergy_scores(ensemblewise_synergies_file) # file_type = "ensemblewise"
data_modelwise = get_synergy_scores(modelwise_synergies_file, file_type = "modelwise")

emba documentation built on Jan. 7, 2021, 9:09 a.m.