emba (version 0.1.8)

get_perf_biomarkers_per_cell_line: Get performance biomarkers per cell line

Description

Use this function to get the performance biomarkers from the respective files inside the given list of directories.

Usage

get_perf_biomarkers_per_cell_line(biomarkers.dirs, node.names)

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 the result data.frame 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).

node.names

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.

Value

a data.frame, whose columns represent the network nodes and the rows the cell lines. Possible values for each cell line-node element are either 1 (active state biomarker), -1 (inhibited state biomarker) or 0 (not a biomarker).

Examples

# NOT RUN {
dir = system.file("extdata", "AGS", "bio", package = "emba", mustWork = TRUE)
res = get_perf_biomarkers_per_cell_line(biomarkers.dirs = c(dir),
  node.names = paste0("x", 1:20))

# }