Man pages for tgrimes/SeqNet
Generate RNA-seq data from regulatory networks

add_sign_to_networkAdd random signs to network edges
add_weight_to_networkAdd random weights to network edges
as.CONFUSIONCoerce a matrix into "CONFUSION" object
as.data.frame.CONFUSIONCoerce "CONFUSION" object into a data.frame
create_networkCreate a network object.
create_network_from_adjacencyCreate a network object from adjacency matrix
fdrDetermine which associations are significant
gen_gamma_poissonGenerate sample from overdispered Poisson
gen_gaussianGenerate sample from a Gaussian graphical model.
gen_gaussian_listGenerate samples from a Gaussian graphical model.
get_adj_matrix_from_networkGet adjacency matrix of a network
get_confusion_matrixGet confusion matrix for predicted classes.
get_degree_changeGet the change in degree for each node between two networks.
get_degree_distributionGet the degree distribution for a network.
get_pathway_listGet a list of pathways in the network
get_reference_count_meansObtain empirical distribution of mean RNA-seq counts
get_sigma_from_precision_listCompute covariance matrices from a list of precision matrices
get_summary_for_nodeGet summary for a node in the network.
isSymmetric.shrinkageTest if a shrinkage object is symmetric.
normalize_cpls_scoresNormalize the cPLS scores
plot.CONFUSIONPlots confusion matrix
plot_networkPlot function for network class
plot.networkPlot function for network class
plot_network_diffPlotting to compare two networks
print.CONFUSIONPrint function for objects of class "CONFUSION"
random_precision_from_network_listGenerate partial correlations for a list of networks.
remove_connections_to_nodeRemove node from the network
remove_node_from_cliqueRemove node from a clique in the network
remove_node_from_hubRemove node from a hub in the network
remove_node_from_moduleRemove node from a module in the network
remove_small_components_from_moduleRemoves small components within a network module.
rewire_connections_to_nodeRewire node in the network.
run_corrWrapper for correlation co-expression
run_cplsCombined partial least squares with negative-binomial
run_cpls_parallelCombined partial least squares with negative-binomial
run_exampleExample of SeqNet package
run_glassoWrapper for glasso method
run_icorrWrapper for inverse covariance matrix
run_pcorWrapper for partial correlations from corpcor
run_wgcnaWrapper for WGCNA method
scores_to_adjacency_matrixInfer adjacency matrix from scores
set_low_rank_scores_to_zeroSet low ranking scores to zero.
summarize_confusionProvides summary measures for confusion matrix
vector_to_matrixTurn a vector into a matrix
tgrimes/SeqNet documentation built on Dec. 1, 2018, 6:55 a.m.