netresponse (version 1.32.2)

get.subnets,NetResponseModel-method: get.subnets

Description

List the detected subnetworks (each is a list of nodes in the corresponding subnetwork).

Usage

## S3 method for class 'NetResponseModel':
get.subnets(model, get.names = TRUE,
  min.size = 2, max.size = Inf, min.responses = 2)

Arguments

model

Output from the detect.responses function. An object of NetResponseModel class.

get.names

Logical. Indicate whether to return subnetwork nodes using node names (TRUE) or node indices (FALSE).

min.size, max.size

Numeric. Filter out subnetworks whose size is not within the limits specified here.

min.responses

Numeric. Filter out subnetworks with less responses (mixture components) than specified here.

Value

• A list of subnetworks.

References

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

Examples

## Load a pre-calculated netresponse model obtained with 
# model <- detect.responses(toydata$emat, toydata$netw, verbose = FALSE)
# data( toydata ); get.subnets(toydata$model)