Protein co-expression network analysis (ProCoNA).

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Documentation for package ‘ProCoNA’ version 1.16.0

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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