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

## Documentation for package ‘PANR’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'