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PANR (version 1.18.0)

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

Description

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

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Version

Version

1.18.0

License

Artistic-2.0

Maintainer

Xin Wang

Last Published

February 15th, 2017

Functions in PANR (1.18.0)

summarize

Summarize the object of S4 class 'BetaMixture' or 'PAN'
data-Bakal2007

Rich morphological phenotypes for gene overexpression and RNA interference screens
viewLegend

View the legends for the graph built for PAN
buildPAN

Build an igraph or RedeR graph for PAN
fitBM

Fit a three-beta mixture model to densities of functional gene associations
cosineSim

Compute cosine similarities or distances between pairs of genes
SNR2p

Translate p-values to Signal-to-Noise Ratios
BetaMixture-class

An S4 class for beta mixture modelling of functional gene associations
pvclustModule

Search enriched functional gene modules by pvclust
assoScore

Association scores for gene pairs
sigModules

Retrieve ids for significant gene modules searched by pvclust
fitNULL

Fit the NULL component of a three-beta mixture model for functional gene associations
p2SNR

Translate p-values to Signal-to-Noise Ratios
infer

Infer a posterior association network
viewNestedModules

View the nested modules in a posterior association network in RedeR
edgeWeight

Compute edge weights for posterior association networks
exportPAN

Export inferred PAN or module graphs to files
permNULL

Do permutations for input rich phenotyping screens.
viewPAN

Show posterior association networks or modules in `igraph' or `RedeR'
view

View the results of beta-mixture model fitting
PAN-class

An S4 class for inferring a posterior association network