infer the S-system gene regulatory network from the gene expression matrix

sfit {ssGrid}

R Documentation

infer the S-system gene regulatory network from the gene expression matrix

Description

Usage

sfit(x,
    opts = NULL,
    prior = NULL,
    time = NULL);

Arguments

the gene expression matrix(rows are genes and columns are the time points), this matrix object could be loaded from a csv file via geneExpression::load.expr. [as Matrix]

opts

the fitting configuration object, see also: ssGrid.sfitOptions(). [as FittingOptions]

prior

the prior knowledge regulatory network, which could be a PriorNetwork object(from bnlearn::as.prior_net or sgrid_prior) or a csv file path. This prior is used as a soft constraint: an interaction that is not supported by the prior will be shrunk, but a new regulation relation could still be discovered from the expression data.

time

the time points of the matrix columns, a numeric vector.

env

the R# runtime environment object. [as Environment]

Authors

biosystem

Value

a SSystemNetwork object that contains the fitted network topology and the kinetic parameters; a R# error message object will be returned if the input data is not valid.

clr value class

SSystemNetwork

Examples

 let opts = sfit_options(sparsity = 0.01, max_edges = 6, smooth = 9);
 let network = sfit(x, opts, prior = as.prior_net(prior_edges), time = t);

[Package ssGrid version 1.0.0.0 Index]