Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations


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Documentation for package ‘PANR’ version 1.22.0

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assoScore Association scores for gene pairs
Bakal2007 Rich morphological phenotypes for gene overexpression and RNA interference screens
Bakal2007Cluster Rich morphological phenotypes for gene overexpression and RNA interference screens
BetaMixture An S4 class for beta mixture modelling of functional gene associations
BetaMixture-class An S4 class for beta mixture modelling of functional gene associations
bm1 Rich morphological phenotypes for gene overexpression and RNA interference screens
buildPAN Build an igraph or RedeR graph for PAN
buildPAN-method Build an igraph or RedeR graph for PAN
cosineDist Compute cosine similarities or distances between pairs of genes
cosineSim Compute cosine similarities or distances between pairs of genes
exportPAN Export inferred PAN or module graphs to files
exportPAN-method Export inferred PAN or module graphs to files
fitBM Fit a three-beta mixture model to densities of functional gene associations
fitBM-method Fit a three-beta mixture model to densities of functional gene associations
fitNULL Fit the NULL component of a three-beta mixture model for functional gene associations
fitNULL-method Fit the NULL component of a three-beta mixture model for functional gene associations
infer Infer a posterior association network
infer-method Infer a posterior association network
nodeColor Rich morphological phenotypes for gene overexpression and RNA interference screens
p2SNR Translate p-values to Signal-to-Noise Ratios
p2SNR-method Translate p-values to Signal-to-Noise Ratios
PAN An S4 class for inferring a posterior association network
PAN-class An S4 class for inferring a posterior association network
pvclustModule Search enriched functional gene modules by pvclust
pvclustModule-method Search enriched functional gene modules by pvclust
sigModules Retrieve ids for significant gene modules searched by pvclust
sigModules-method Retrieve ids for significant gene modules searched by pvclust
SNR2p Translate p-values to Signal-to-Noise Ratios
SNR2p-method Translate p-values to Signal-to-Noise Ratios
summarize Summarize the object of S4 class 'BetaMixture' or 'PAN'
summarize-method Summarize the object of S4 class 'BetaMixture' or 'PAN'
view View the results of beta-mixture model fitting
view-method View the results of beta-mixture model fitting
viewLegend View the legends for the graph built for PAN
viewLegend-method View the legends for the graph built for PAN
viewNestedModules View the nested modules in a posterior association network in RedeR
viewNestedModules-method View the nested modules in a posterior association network in RedeR
viewPAN Show posterior association networks or modules in 'igraph' or 'RedeR'
viewPAN-method Show posterior association networks or modules in 'igraph' or 'RedeR'