sample.chain: Random initial network edge generation

In anna-pacinkova/intomics_package: Integrative analysis of multi-omics data to infer regulatory networks

Random initial network edge generation

Description

sample.chain This function is used to sample random initial network. The edges are sampled only between GE nodes.

Usage

sample.chain(empty_net, omics_ge)

Arguments

empty_net	adjacency matrix of an empty network/graph (all values are 0).
omics_ge	matrix with gene expression data (samples in rows and features in columns).

Value

BN object with conditional probabilities

Examples

data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics"),
package="IntOMICS")
B <- B_prior_mat(omics = omics, PK = PK, layers_def = layers_def, 
     annot = annot, lm_METH = TRUE, r_squared_thres = 0.3,
     p_val_thres = 0.05, TFtargs = TFtarg_mat, TFBS_belief = 0.75, 
     nonGE_belief = 0.5, woPKGE_belief = 0.5)
empty.net <- matrix(0, nrow = sum(mapply(ncol,B$omics)), ncol =
sum(mapply(ncol,B$omics)), dimnames = list(unlist(mapply(colnames,B$omics)),
unlist(mapply(colnames,B$omics))))
sample.chain(empty_net = empty.net, 
     omics_ge = B$omics[[layers_def$omics[1]]])

anna-pacinkova/intomics_package documentation built on Aug. 13, 2022, 11:38 a.m.