get_synergy_biomarkers_per_cell_line: Get synergy biomarkers per cell line

In emba: Ensemble Boolean Model Biomarker Analysis

Description

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.

Usage

get_synergy_biomarkers_per_cell_line(biomarkers.dirs)

Arguments

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} (the directory name does not matter, but 'biomarkers' is a good choice), 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.

Value

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).

Examples

dir = system.file("extdata", "AGS", "bio", package = "emba", mustWork = TRUE)
res_list = get_synergy_biomarkers_per_cell_line(biomarkers.dirs = c(dir))

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