nem_Tar_triples: Inferring the signaling network from (epi)genetic aberrations...

In CityUHK-CompBio/nemTar: A method for singlaing network inference from (epi)genetic aberration profiles

Description

Inferring the signaling network from (epi)genetic aberrations and effect reporter gene profiles based on triple realtion inference methods

Usage

nem_Tar_triples(D, Sgenes, S_pattern, control, verbose = TRUE)

Arguments

D	an E-gene observation matrix with the dimension of p(number of samples) × n(number of effect reporter genes)
Sgenes	a character vector of S-genes
S_pattern	a binary matrix showing the state of whether signaling components(S-genes)are perturbed, with the dimension of m × m(m is the number of S-genes)
control	a list contains necessary parameters for implementing the methods,as nemTar is developed based on nem, the users of nemTar should apply the function nem::set.default.parameters(Sgenes,type="mLL",para=para), para is a vector of length two:false positive rate and false negative rate.
verbose	a logic to whether present the execution process

Value

a list contains the network inference results using triple relation, please also refer to the nem

See Also

nem_Tar_greedy nem

CityUHK-CompBio/nemTar documentation built on March 11, 2021, 6:03 p.m.