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.

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.