netresponse (version 1.32.2)

get.model.parameters: get.model.parameters

Description

Retrieve the mixture model parameters of the NetResponse algorithm for a given subnetwork.

Usage

get.model.parameters(model, subnet.id = NULL)

Arguments

model

Result from NetResponse (detect.responses function).

subnet.id

Subnet identifier. A natural number which specifies one of the subnetworks within the 'model' object.

Value

• A list with the following elements:
• mu
  Centroids for the mixture components. Components x nodes.
• sd
  Standard deviations for the mixture components. A vector over the nodes for each component, implying the diagonal covariance matrix of the model (i.e. diag(std^2)). Components x nodes
• w
  Vector of component weights.
• nodes
  List of nodes in the subnetwork.
• K
  Number of mixture components.

Details

Only the non-empty components are returned. Note: the original data matrix needs to be provided for function call separately.

References

Leo Lahti et al.: Global modeling of transcriptional responses in interaction networks. Bioinformatics (2010). See citation("netresponse") for details.

Examples

# Load toy data
data( toydata )          # Load toy data set
D     <- toydata$emat    # Response matrix (for example, gene expression)
model <- toydata$model   # Pre-calculated model

# Get model parameters for a given subnet
# (Gaussian mixture: mean, covariance diagonal, mixture proportions)
get.model.parameters(model, subnet.id = 1)