This function applies ARACNE on the data

This function takes in a gene expression matrix of gene expression and applies the ARACNE gene co-expression network analysis frame work to find coexpressed gene pairs in the matrix. The ARACNE framework is also installed from within the package located in the `inst/tools/` direcctory. For more information on the ARACNE framework see: <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-S1-S7>

Usage

aracne(
  data,
  path = NULL,
  pval = NULL,
  outputpath,
  na_fill = NULL,
  tool_storage_loc
)

Arguments

data

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

path

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

pval

Optional. Cutoff p-value to determine a coexpressed edge. (Default = 0.05)

outputpath

Required. The path the resulting network should be saved to.

na_fill

Optional. Value to replace `NA` values with ideally, a large negative number or use min(data). (Default = NULL)

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

A Co-Expression Network saved to the path `outputpath` and titled `aracneThresholdNetwork.csv` (if `pval` < 1) or as `aracneNetwork.csv` if `pval` is set to 1.