Skip to contents

Implements mrnet

Source: R/mrnetWrapper.R
mrnetWrapper.Rd

This function infers the interaction network of `data` using the MRNET algorithm.

Usage

mrnetWrapper(
  data,
  temp_path,
  path = NULL,
  pval = 1,
  outputpath,
  tool_storage_loc
)

Arguments

data

Required. A gene expression matrix with rows as sample IDs and columns as Gene or feature IDs.

temp_path

Required. The path location to install aracne to. eg. `config$input_profile$temp_storage_loc`

path

Optional. String containing the path to the aracne compiled executable. (Default = NULL)

pval

Optional. Cutoff p-value to determine a coexpressed edge. If one is specified aracne will produce the file `aracneNetwork.csv` if less than 1 it will produce the file `aracneThresholdNetwork.csv`. (Default = 1)

outputpath

Required. The output path to save the resulting coexpression network

tool_storage_loc

Required. Provides the directory inside docker to temporarily store the ARACNE files and package. (Default = config$input_profile$temp_storage_loc)

Value

NULL. Saves a sparrow network object to paste0(`outputpath`, `regressionFunction`,'mrnetNetwork.csv')