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

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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.

Author
Xin Wang <xin_wang@hms.harvard.edu>
Date of publication
None
Maintainer
Xin Wang <xin_wang@hms.harvard.edu>
License
Artistic-2.0
Version
1.20.0

View on Bioconductor

Man pages

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

Files in this package

PANR/DESCRIPTION
PANR/NAMESPACE
PANR/R
PANR/R/AllClasses.R
PANR/R/AllGenerics.R
PANR/R/BetaMixture-methods.R
PANR/R/PAN-methods.R
PANR/R/assoScore.R
PANR/R/classUnions.R
PANR/R/panGraphics.R
PANR/build
PANR/build/vignette.rds
PANR/data
PANR/data/Bakal2007.RData
PANR/data/Bakal2007Cluster.RData
PANR/data/bm.RData
PANR/data/datalist
PANR/inst
PANR/inst/CHANGES
PANR/inst/NEWS
PANR/inst/doc
PANR/inst/doc/PANR-Vignette.R
PANR/inst/doc/PANR-Vignette.Rnw
PANR/inst/doc/PANR-Vignette.pdf
PANR/man
PANR/man/BetaMixture-class.Rd
PANR/man/PAN-class.Rd
PANR/man/SNR2p.Rd
PANR/man/assoScore.Rd
PANR/man/buildPAN.Rd
PANR/man/cosineSim.Rd
PANR/man/data-Bakal2007.Rd
PANR/man/edgeWeight.Rd
PANR/man/exportPAN.Rd
PANR/man/fitBM.Rd
PANR/man/fitNULL.Rd
PANR/man/infer.Rd
PANR/man/p2SNR.Rd
PANR/man/permNULL.Rd
PANR/man/pvclustModule.Rd
PANR/man/sigModules.Rd
PANR/man/summarize.Rd
PANR/man/view.Rd
PANR/man/viewLegend.Rd
PANR/man/viewNestedModules.Rd
PANR/man/viewPAN.Rd
PANR/vignettes
PANR/vignettes/PANR-Vignette.Rnw
PANR/vignettes/fullPAN.pdf
PANR/vignettes/overview.png
PANR/vignettes/pvmodule.pdf
PANR/vignettes/sigmod.pdf