netresponse (version 1.32.2)

response2sample: response2sample

Description

List the most strongly associated response of a given subnetwork for each sample.

Usage

response2sample(model, subnet.id = NULL, component.list = TRUE,
  verbose = FALSE, data = NULL)

Arguments

model

A NetResponseModel object or list.

subnet.id

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

component.list

List samples separately for each mixture component (TRUE). Else list the most strongly associated component for each sample (FALSE).

verbose

Follow progress by intermediate messages.

data

Data (features x samples; or a vector for univariate case) to predict response for given data points (currently implemented only for mixture.model output)

Return:

Value

• A list. Each element corresponds to one subnetwork response, and contains a list of samples that are associated with the response (samples for which this response has the highest probability P(response | sample)).

References

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

Examples

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

# Find the samples for each response (for a given subnetwork)
response2sample(model, subnet.id = 1)