detect.responses: detect.responses

In antagomir/netresponse: Functional Network Analysis

detect.responses

Description

Main function of the NetResponse algorithm. Detect condition-specific network responses, given network and a set of measurements of node activity in a set of conditions. Returns a set of subnetworks and their estimated context-specific responses.

Usage

detect.responses(
  datamatrix,
  network = NULL,
  initial.responses = 1,
  max.responses = 10,
  max.subnet.size = 10,
  verbose = TRUE,
  prior.alpha = 1,
  prior.alphaKsi = 0.01,
  prior.betaKsi = 0.01,
  update.hyperparams = 0,
  implicit.noise = 0,
  vdp.threshold = 1e-05,
  merging.threshold = 0,
  ite = Inf,
  information.criterion = "BIC",
  speedup = TRUE,
  speedup.max.edges = 10,
  positive.edges = FALSE,
  mc.cores = 1,
  mixture.method = "vdp",
  bic.threshold = 0,
  pca.basis = FALSE,
  ...
)

Arguments

datamatrix	Matrix of samples x features. For example, gene expression matrix with conditions on the rows, and genes on the columns. The matrix contains same features than the 'network' object, characterizing the network states across the different samples.
network	Binary network describing undirected pairwise interactions between features of 'datamatrix'. The following formats are supported: binary matrix, graphNEL, igraph, graphAM, Matrix, dgCMatrix, dgeMatrix
initial.responses	Initial number of components for each subnetwork model. Used to initialize calculations.
max.responses	Maximum number of responses for each subnetwork. Can be used to limit the potential number of network states.
max.subnet.size	Numeric. Maximum allowed subnetwork size.
verbose	Logical. Verbose parameter.
prior.alpha, prior.alphaKsi, prior.betaKsi	Prior parameters for Gaussian mixture model that is calculated for each subnetwork (normal-inverse-Gamma prior). alpha tunes the mean; alphaKsi and betaKsi are the shape and scale parameters of the inverse Gamma function, respectively.
update.hyperparams	Logical. Indicate whether to update hyperparameters during modeling.
implicit.noise	Implicit noise parameter. Add implicit noise to vdp mixture model. Can help to avoid overfitting to local optima, if this appears to be a problem.
vdp.threshold	Minimal free energy improvement after which the variational Gaussian mixture algorithm is deemed converged.
merging.threshold	Minimal cost value improvement required for merging two subnetworks.
ite	Defines maximum number of iterations on posterior update (updatePosterior). Increasing this can potentially lead to more accurate results, but computation may take longer.
information.criterion	Information criterion for model selection. Default is BIC (Bayesian Information Criterion); other options include AIC and AICc.
speedup	Takes advantage of approximations to PCA, mutual information etc in various places to speed up calculations. Particularly useful with large and densely connected networks and/or large sample size.
speedup.max.edges	Used if speedup = TRUE. Applies prefiltering of edges for calculating new joint models between subnetwork pairs when potential cost changes (delta) are updated for a newly merged subnetwork and its neighborghs. Empirical mutual information between each such subnetwork pair is calculated based on their first principal components, and joint models will be calculated only for the top candidates up to the number specified by speedup.max.edges. It is expected that the subnetwork pair that will benefit most from joint modeling will be among the top mutual infomation candidates. This way it is possible to avoid calculating exhaustive many models on the network hubs.
positive.edges	Consider only the edges with positive association. Currently measured with Spearman correlation.
mc.cores	Number of cores to be used in parallelization. See help(mclapply) for details.
mixture.method	Specify the approach to use in mixture modeling. Options. vdp (nonparametric Variational Dirichlet process mixture model); bic (based on Gaussian mixture modeling with EM, using BIC to select the optimal number of components)
bic.threshold	BIC threshold which needs to be exceeded before a new mode is added to the mixture with mixture.method = "bic"
pca.basis	Transform data first onto PCA basis to try to avoid problems with non-diagonal covariances.
...	Further optional arguments to be passed.

Value

NetResponseModel object.

Author(s)

Maintainer: Leo Lahti [e-mail]

References

See citation("netresponse").

Examples

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

# Run NetReponse algorithm
# model <- detect.responses(D, netw, verbose = FALSE)

antagomir/netresponse documentation built on March 30, 2023, 7:24 a.m.