cosmos_data {cosmosR} | R Documentation

## Create Cosmos Data

### Description

An S3 class that combines the required data into a comprehensive list. Use the `preprocess_COSMOS_signaling_to_metabolism` or `preprocess_COSMOS_metabolism_to_signaling` to create an instance.

### Usage

    cosmos_data(
      meta_network,
      tf_regulon = NULL,
      signaling_data,
      metabolic_data,
      expression_data,
      verbose = TRUE
    )

### Arguments

`meta_network` | Prior knowledge network (PKN). By default COSMOS use a PKN derived from Omnipath, STITCHdb and Recon3D. See details on the data `meta_network`.
`tf_regulon` | Collection of transcription factor - target interactions. A default collection from dorothea can be obtained by the `load_tf_regulon_dorothea` function.
`signaling_data` | Numerical vector, where names are signaling nodes in the PKN and values are from {1, 0, -1}. Continuous data will be discretized using the `sign` function.
`metabolic_data` | Numerical vector, where names are metabolic nodes in the PKN and values are continuous values that represents log2 fold change or t-values from a differential analysis. These values are compared to the simulation results (simulated nodes can take value -1, 0 or 1).
`expression_data` | Numerical vector that represents the results of a differential gene expression analysis. Names are gene names using EntrezID starting with an X and values are log fold change or t-values. Genes with NA values are considered none expressed and they will be removed from the TF-gene expression interactions.
`verbose` | (default: TRUE) Reports details about the `cosmos_data` object.

### Value

`cosmos data` class instance.

[Package cosmosR version 1.2.0 Index]