The main function to perform model learning from data
Usage
nem(D,inference="nem.greedy",models=NULL,control=set.default.parameters(setdiff(unique(colnames(D)),"time")), verbose=FALSE)
## S3 method for class 'nem'
print(x, ...)
Arguments
D
data matrix with experiments in the columns (binary or continious)
inference
search to use exhaustive enumeration, triples for triple-based inference, pairwise for the pairwise heuristic,
ModuleNetwork for the module based inference proposed in Fr"ohlich et al. 2008, ModuleNetwork.orig for the module based inference proposed in Fr"ohlich et al. 2007, nem.greedy for greedy hillclimbing, nem.greedyMAP for alternating MAP optimization using log odds or log p-value densities, mc.eminem for EM based inference using log odds or log p-value densities, BN.greedy, BN.exhaustive for a conventional Bayesian Network treatment using binomial or normal distribution assumptions, dynoNEM for MCMC based inference from time series data, mc.eminem for EM based inference
models
a list of adjacency matrices for model search. If NULL, an exhaustive enumeration of all possible models is performed.
control
list of parameters: see set.default.parameters
verbose
do you want to see progression statements? Default: TRUE
x
nem object
...
other arguments to pass
Details
If parameter Pm != NULL and parameter lambda == 0, a Bayesian approach to include prior knowledge is used. Alternatively, the regularization parameter lambda can be tuned in a model selection step via the function nemModelSelection using the BIC criterion.
If automated subset selection of effect reporters is used (default), the regularization parameter delta can be tuned via the BIC model selection criterion. Per default it is fixed to 1 / (no. S-genes + 1).
The function plot.nem plots the inferred phenotypic hierarchy as a directed graph, the likelihood distribution of the models (only for exhaustive search) or the posterior position of the effected genes.
Value
graph
inferred directed S-gene graph (graphNEL object)
mLL
log posterior marginal likelihood of model(s)
pos
posterior over effect positions
mappos
MAP estimate of effect positions
selected
selected E-gene subset
LLperGene
likelihood per selected E-gene
avg
in case of MCMC: posterior mean S-gene graph (edge weighted adjacency matrix)
control
hyperparameter as in function call
For inference = "mc.eminem" the following additional values are returned:
local.maxima
local maxima of the EM procedure
graphs.sampled
sampled graphs
EB
samples of the empirical Bayes prior
acc_list
list that indicates whether the corresponding sampled S-gene graph has been accepted (new local maximum (1), same local maximum (0)) or rejected(-1) in the MCMC sampling process - length(acc_list)=mcmc.nsamples + mcmc.nburnin
Author(s)
Holger Froehlich, Florian Markowetz
References
Markowetz, F.; Bloch, J. & Spang, R., Non-transcriptional Pathway Features Reconstructed from Secondary Effects of RNA interference. Bioinformatics, 2005, 21, 4026 - 4032
Markowetz, F.; Kostka, D.; Troyanskaya, O. & Spang, R., Nested Effects Models for High-dimensional Phenotyping Screens. Bioinformatics, 2007, 23, i305 - i312
Fr"ohlich, H.; Fellmann, M.; S"ultmann, H.; Poustka, A. & Beissbarth, T. Large Scale Statistical Inference of Signaling Pathways from RNAi and Microarray Data. BMC Bioinformatics, 2007, 8, 386
Fr"ohlich, H.; Fellmann, M.; S"ultmann, H.; Poustka, A. & Beissbarth, T. Estimating Large Scale Signaling Networks through Nested Effect Models with Intervention Effects from Microarray Data. Bioinformatics, 2008, 24, 2650-2656
Tresch, A. & Markowetz, F., Structure Learning in Nested Effects Models Statistical Applications in Genetics and Molecular Biology, 2008, 7
Zeller, C.; Fr"ohlich, H. & Tresch, A., A Bayesian Network View on Nested Effects Models EURASIP Journal on Bioinformatics and Systems Biology, 2009, 195272
Fr"ohlich, H.; Tresch, A. & Beissbarth, T., Nested Effects Models for Learning Signaling Networks from Perturbation Data. Biometrical Journal, 2009, 2, 304 - 323
Fr"ohlich, H.; Sahin, "O.; Arlt, D.; Bender, C. & Beissbarth, T. Deterministic Effects Propagation Networks for Reconstructing Protein Signaling Networks from Multiple Interventions. BMC Bioinformatics, 2009, 10, 322
Fr"ohlich, H.; Praveen, P. & Tresch, A., Fast and Efficient Dynamic Nested Effects Models. Bioinformatics, 2011, 27, 238-244
Niederberger, T.; Etzold, S.; Lidschreiber, M; Maier, K.; Martin, D.; Fr"ohlich, H.; Cramer, P.; Tresch, A., MC Eminem Maps the Interaction Landscape of the Mediator, PLoS Comp. Biol., 8(6): e1002568, 2012.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(nem)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/nem/nem.Rd_%03d_medium.png", width=480, height=480)
> ### Name: nem
> ### Title: Nested Effects Models - main function
> ### Aliases: nem print.nem print.nem.greedy print.nem.greedyMAP
> ### print.pairwise print.triples print.ModuleNetwork print.score
> ### print.nem.BN print.mc.eminem print.dynoNEM
> ### Keywords: graphs models
>
> ### ** Examples
>
> data("BoutrosRNAi2002")
> D <- BoutrosRNAiDiscrete[,9:16]
> control = set.default.parameters(unique(colnames(D)), para=c(0.13, 0.05))
> res1 <- nem(D,inference="search", control=control)
> res2 <- nem(D,inference="pairwise", control=control)
> res3 <- nem(D,inference="triples", control=control)
4 perturbed genes -> 4 triples to check (lambda = 0 )
> res4 <- nem(D,inference="ModuleNetwork", control=control)
Estimating module network of 4 S-genes (lambda = 0 )...
> res5 <- nem(D,inference="nem.greedy", control=control)
Greedy hillclimber for 4 S-genes (lambda = 0 )...
> res6 = nem(BoutrosRNAiLods, inference="nem.greedyMAP", control=control)
Alternating optimization for 4 S-genes (lambda = 0 )...
>
>
> par(mfrow=c(2,3))
> plot.nem(res1,main="exhaustive search")
> plot.nem(res2,main="pairs")
> plot.nem(res3,main="triples")
> plot.nem(res4,main="module network")
> plot.nem(res5,main="greedy hillclimber")
> plot.nem(res6,main="alternating MAP optimization")
>
>
>
>
>
> dev.off()
null device
1
>