# Protein co-expression network analysis (ProCoNA).

## Documentation for package ‘ProCoNA’ version 1.12.0

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

## Help Pages

A B C D G H I M N O P R S T U

procona-package | Peptide co-expression network construction.

## -- A --

adj | Accessors for the proconaNet S4 class
adj-method | Accessors for the proconaNet S4 class
adj<- | Accessors for the proconaNet S4 class
adj<--method | Accessors for the proconaNet S4 class

## -- B --

bootstrapProconaNetwork | bootstrapProconaNetwork
buildProconaNetwork | buildProconaNetwork

## -- C --

c2i | c2i
colorOrder | Accessors for the proconaNet S4 class
colorOrder-method | Accessors for the proconaNet S4 class
colorOrder<- | Accessors for the proconaNet S4 class
colorOrder<--method | Accessors for the proconaNet S4 class
compareNetworksWithFishersExactTest | compareNetworksWithFishersExactTest
compareNetworksWithFishersExactTest-method | compareNetworksWithFishersExactTest
compareNetworksWithFishersExactTestProcona | compareNetworksWithFishersExactTestProcona
compareNetworksWithFishersExactTestProcona-method | compareNetworksWithFishersExactTestProcona
corBootstrap | corBootstrap
correlationWithPhenotypesHeatMap | correlationWithPhenotypesHeatMap
correlationWithPhenotypesHeatMap-method | correlationWithPhenotypesHeatMap

## -- D --

dynamicColors | Accessors for the proconaNet S4 class
dynamicColors-method | Accessors for the proconaNet S4 class
dynamicColors<- | Accessors for the proconaNet S4 class
dynamicColors<--method | Accessors for the proconaNet S4 class

## -- G --

getFisherMatrix | getFisherMatrix
getFisherMatrix-method | getFisherMatrix
getPeptideNAs | getPeptideNAs
goStatTest | goStatTest
goStatTest-method | goStatTest

## -- H --

hclust-class | Class '"hclust"'

## -- I --

i2c | i2c
i2col | i2col

## -- M --

masstagdb | A simulated mass tag data base
mergedColors | Accessors for the proconaNet S4 class
mergedColors-method | Accessors for the proconaNet S4 class
mergedColors<- | Accessors for the proconaNet S4 class
mergedColors<--method | Accessors for the proconaNet S4 class
mergedMEs | Accessors for the proconaNet S4 class
mergedMEs-method | Accessors for the proconaNet S4 class
mergedMEs<- | Accessors for the proconaNet S4 class
mergedMEs<--method | Accessors for the proconaNet S4 class
MEs | Accessors for the proconaNet S4 class
MEs-method | Accessors for the proconaNet S4 class
MEs<- | Accessors for the proconaNet S4 class
MEs<--method | Accessors for the proconaNet S4 class
MMvsPS | Module members vs Peptide Significance
MMvsPS-method | Module members vs Peptide Significance
MMvsPSallModules | MMvsPSallModules
MMvsPSallModules-method | MMvsPSallModules
moduleMemberCorrelations | moduleMemberCorrelations
moduleMemberCorrelations-method | moduleMemberCorrelations
modulePhenotypeCorrelations | modulePhenotypeCorrelations
modulePhenotypeCorrelations-method | modulePhenotypeCorrelations

## -- N --

net1 | A simulated mass tag data base
net2 | A simulated mass tag data base
networkName | Accessors for the proconaNet S4 class
networkName-method | Accessors for the proconaNet S4 class
networkName<- | Accessors for the proconaNet S4 class
networkName<--method | Accessors for the proconaNet S4 class
networkPower | Accessors for the proconaNet S4 class
networkPower-method | Accessors for the proconaNet S4 class
networkPower<- | Accessors for the proconaNet S4 class
networkPower<--method | Accessors for the proconaNet S4 class
networkType | Accessors for the proconaNet S4 class
networkType-method | Accessors for the proconaNet S4 class
networkType<- | Accessors for the proconaNet S4 class
networkType<--method | Accessors for the proconaNet S4 class

## -- O --

orderMatrixIndex | orderMatrixIndex

## -- P --

pepnet | Accessors for the proconaNet S4 class
pepnet-class | Accessors for the proconaNet S4 class
peptideConnectivityTest | peptideConnectivityTest
peptideConnectivityTest-method | peptideConnectivityTest
peptideCorrelationTest | peptideCorrelationTest
peptideCorrelationTest-method | peptideCorrelationTest
peptideData | A simulated mass tag data base
peptides | Accessors for the proconaNet S4 class
peptides-method | Accessors for the proconaNet S4 class
peptides<- | Accessors for the proconaNet S4 class
peptides<--method | Accessors for the proconaNet S4 class
pepTree | Accessors for the proconaNet S4 class
pepTree-method | Accessors for the proconaNet S4 class
pepTree<- | Accessors for the proconaNet S4 class
pepTree<--method | Accessors for the proconaNet S4 class
permtest | Accessors for the proconaNet S4 class
permtest-method | Accessors for the proconaNet S4 class
permtest<- | Accessors for the proconaNet S4 class
permtest<--method | Accessors for the proconaNet S4 class
phenotypes | A simulated mass tag data base
plotNet | plotNet
power | Accessors for the proconaNet S4 class
power-method | Accessors for the proconaNet S4 class
power<- | Accessors for the proconaNet S4 class
power<--method | Accessors for the proconaNet S4 class
ppiPermTest | ppiPermTest
ppiPermTest-method | ppiPermTest
print-method | proconaNet S4 class
printNet | printNet
proconaNet | proconaNet S4 class
proconaNet-class | proconaNet S4 class
proconaVersion | Accessors for the proconaNet S4 class
proconaVersion-method | Accessors for the proconaNet S4 class
proconaVersion<- | Accessors for the proconaNet S4 class
proconaVersion<--method | Accessors for the proconaNet S4 class
proconaVersionFun | Procona Software Version

## -- R --

runningStats | runningStats

## -- S --

samples | Accessors for the proconaNet S4 class
samples,proconaNet-methods | Accessors for the proconaNet S4 class
samples-method | Accessors for the proconaNet S4 class
samples<- | Accessors for the proconaNet S4 class
samples<-,proconaNet-methods | Accessors for the proconaNet S4 class
samples<--method | Accessors for the proconaNet S4 class
show-method | proconaNet S4 class
subsetModCors | subsetModCors
subsetPeptideData | subsetPeptideData

## -- T --

TOM | Accessors for the proconaNet S4 class
TOM-method | Accessors for the proconaNet S4 class
TOM<- | Accessors for the proconaNet S4 class
TOM<--method | Accessors for the proconaNet S4 class
toPermTest | toPermTest
toPermTest-method | toPermTest

## -- U --

universe | A simulated mass tag data base
utri | utri