mogamun_load_data: mogamun_load_data

In elvanov/MOGAMUN: MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Description

Load the data to process

Usage

mogamun_load_data(
    EvolutionParameters,
    DifferentialExpressionPath,
    NodesScoresPath,
    NetworkLayersDir,
    Layers
)

Arguments

EvolutionParameters	evolution paramenters returned by mogamun_init()
DifferentialExpressionPath	full path to the differential expression results file (in CSV format). This file must contain at least the columns "gene" with the gene names, and ("PValue" or "FDR"). It can also contain "logFC"
NodesScoresPath	full path to an existing CSV file containing the nodes scores (columns "gene" and "nodescore"). NOTE. If the file does not exist, MOGAMUN will generate it in the provided path with the specified name
NetworkLayersDir	path of the folder that contains the networks that will be the layers of the multiplex. NOTE. Each file must start with a different digit
Layers	string of numbers, where the numbers correspond to the first character of the name of the network files (e.g. "123" builds a multiplex with layers 1, 2, and 3)

Value

List with the data to process

Examples

DEGPath <- system.file("extdata/DE/Sample_DE.csv", package = "MOGAMUN")
NodesScoresPath <- 
    system.file("extdata/DE/Sample_NodesScore.csv", package = "MOGAMUN")
LayersPath <- 
    paste0(system.file("extdata/LayersMultiplex", package = "MOGAMUN"), "/")
EvolutionParameters <- mogamun_init(Generations = 1, PopSize = 10)
LoadedData <- 
    mogamun_load_data(
        EvolutionParameters = EvolutionParameters,
        DifferentialExpressionPath = DEGPath,
        NodesScoresPath = NodesScoresPath,
        NetworkLayersDir = LayersPath,
        Layers = "23"
    )

elvanov/MOGAMUN documentation built on Oct. 26, 2021, 3:14 p.m.