maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis
Version 1.40.0

This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data

Browse man pages Browse package API and functions Browse package files

AuthorGustavo H. Esteves <gesteves@gmail.com>, with contributions from Roberto Hirata Jr <hirata@ime.usp.br>, E. Jordao Neves <neves@ime.usp.br>, Elier B. Cristo <elier@ime.usp.br>, Ana C. Simoes <anakqui@ime.usp.br> and Lucas Fahham <fahham@linux.ime.usp.br>
Bioconductor views Classification Clustering DifferentialExpression GraphAndNetwork Microarray Preprocessing ThirdPartyClient TwoChannel
Date of publicationNone
MaintainerGustavo H. Esteves <gesteves@gmail.com>
LicenseGPL (>= 2)
Version1.40.0
URL http://www.maiges.org/en/software/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("maigesPack")

Man pages

activeMod: Functional classification of gene groups
activeModScoreHTML: Save HTML file with global gene scores from functional gene...
activeNet: Functional classification of gene networks
activeNetScoreHTML: Save HTML file with scores and p-values from functional gene...
addGeneGrps: Function to load gene groups into maigesPreRaw object
addPaths: Function to load gene pathways into maigesPreRaw object
bootstrapCor: Calculate bootstrap p-values for correlation measures
bootstrapMI: Calculate bootstrap p-values for mutual information (MI)...
bootstrapT: Calculate bootstrap p-values for t statistics
boxplot-methods: Method boxplot for objects defined in this package
bracketMethods: Sub-setting methods for maiges objects
calcA: Method calcA to calculate A values
calcW: Method calcW to calculate W values
classifyKNN: Function to do discrimination analysis
classifyKNNsc: Function to do discrimination analysis, by the search and...
classifyLDA: Function to do discrimination analysis
classifyLDAsc: Function to do discrimination analysis, by the search and...
classifySVM: Function to do discrimination analysis
classifySVMsc: Function to do discrimination analysis, by the search and...
coerce-methods: Coerce a maiges object to classes defined by packages limma...
compCorr: Compute correlation differences and their p-values
contrastsFitM: Compute Contrasts from Linear Model Fit
createMaigesRaw: Function to create objects of class maigesRaw
createTDMS: Create a tab delimited file for TIGR MeV
deGenes2by2BootT: Function to do differential expression analysis, comparing...
deGenes2by2Ttest: Function to do differential expression analysis, comparing...
deGenes2by2Wilcox: Function to do differential expression analysis, comparing...
deGenesANOVA: Function to do differential expression analysis, using ANOVA...
designANOVA: Function to construct design an contrasts matrices for ANOVA...
dim-methods: Retrieve the dimension of microarray objects
gastro: Gastro-esophagic dataset
getLabels: Method getLabels to pick gene and sample labels
heatmapsM: Function to plot heatmaps separating groups generated by SOM...
hierM: Function to do hierarchical cluster analysis
hierMde: Function to do hierarchical cluster analysis
image-methods: Method image for objects defined in this package
kmeansM: Function to do k-means cluster analysis
kmeansMde: Function to do k-means cluster analysis
loadData: Load cDNA microarray data tables
maigesActMod-class: maigesActMod class, store results of functional...
maigesActNet-class: maigesActNet class, store results of functional...
maigesANOVA-class: maigesANOVA class, extend maiges class to fit ANOVA models
maiges-class: maiges class, store normalised microarray datasets
maigesClass-class: maigesClass class, store results of discrimination (or...
maigesDE-class: maigesDE class, store results of differential gene expression...
maigesDEcluster-class: maigesDEcluster class, store results of differential gene...
maigesPreRaw-class: maigesPreRaw class, store pre raw microarray datasets
maigesRaw-class: maigesRaw class, store raw microarray datasets
maigesRelNetB-class: maigesRelNetB class, store results of relevance network...
maigesRelNetM-class: maigesRelNetM class, store results of relevance network...
MI: Calculate Mutual Information
normLoc: Normalise a cDNA Microarray Object
normOLIN: Normalise a cDNA Microarray Object
normRepLoess: Bootstrap of LOWESS normalisation
normScaleLimma: Scale adjust a cDNA Microarray Object
normScaleMarray: Scale adjust a cDNA Microarray Object
plotGenePair: Scatter plots for pair of genes
plot-methods: Method plot for objects defined in this package
print-methods: Method to print a nice visualisation of the objects defined...
relNet2TGF: Transform Relevance Network analysis in TGF output
relNetworkB: Relevance Network analysis
relNetworkM: Relevance Network analysis
robustCorr: Calculate a robust correlation value
selSpots: Select spots to use in normalisation
show-methods: Show a nice visualisation of the objects defined in this...
somM: Function to do SOM cluster analysis
somMde: Function to do SOM cluster analysis
summarizeReplicates: Summarise microarray objects
summary-methods: Method summary for the object from this package
tableClass: Save HTML or CSV tables of good classifiers (cliques)
tablesDE: Save HTML or CSV tables of differentially expressed genes

Functions

MI Man page Source code
[ Man page
[,maiges-method Man page
[,maigesANOVA-method Man page
[,maigesPreRaw-method Man page
[,maigesRaw-method Man page
activeMod Man page Source code
activeModScoreHTML Man page Source code
activeNet Man page Source code
activeNetScoreHTML Man page Source code
addGeneGrps Man page Source code
addPaths Man page Source code
as Man page
as,MAList,maiges-method Man page
as,RGList,maigesRaw-method Man page
as,maiges,MAList-method Man page
as,maiges,marrayNorm-method Man page
as,maigesRaw,RGList-method Man page
as,maigesRaw,marrayRaw-method Man page
as,marrayNorm,maiges-method Man page
as,marrayRaw,maigesRaw-method Man page
blackBlue Source code
bootstrapCor Man page Source code
bootstrapMI Man page Source code
bootstrapT Man page Source code
boxplot Man page
boxplot.maiges Man page Source code
boxplot.maigesANOVA Man page
boxplot.maigesDEcluster Man page Source code
boxplot.maigesRaw Man page Source code
calcA Man page Source code
calcA.default Man page Source code
calcA.maigesRaw Man page Source code
calcW Man page Source code
calcW.default Man page Source code
calcW.maigesRaw Man page Source code
classifyKNN Man page Source code
classifyKNNsc Man page Source code
classifyLDA Man page Source code
classifyLDAsc Man page Source code
classifySVM Man page Source code
classifySVMsc Man page Source code
coerce,MAList,maiges-method Man page
coerce,RGList,maigesRaw-method Man page
coerce,maiges,MAList-method Man page
coerce,maiges,marrayNorm-method Man page
coerce,maigesRaw,RGList-method Man page
coerce,maigesRaw,marrayRaw-method Man page
coerce,marrayNorm,maiges-method Man page
coerce,marrayRaw,maigesRaw-method Man page
compCorr Man page Source code
contrastsFitM Man page Source code
createMaigesRaw Man page Source code
createTDMS Man page Source code
deGenes2by2BootT Man page Source code
deGenes2by2Ttest Man page Source code
deGenes2by2Wilcox Man page Source code
deGenesANOVA Man page Source code
designANOVA Man page Source code
dim.maiges Man page Source code
dim.maigesANOVA Man page Source code
dim.maigesPreRaw Man page Source code
dim.maigesRaw Man page Source code
gastro Man page
gastro.norm Man page
gastro.raw Man page
gastro.raw2 Man page
gastro.summ Man page
getLabels Man page Source code
getLabels.MAList Man page Source code
getLabels.RGList Man page Source code
getLabels.default Man page Source code
getLabels.maigesDE Man page Source code
getLabels.maigesDEcluster Man page
getLabels.marrayNorm Man page Source code
getLabels.marrayRaw Man page Source code
greenRed Source code
heatmapsM Man page Source code
hierM Man page Source code
hierMde Man page Source code
image Man page
image.maiges Man page Source code
image.maigesANOVA Man page
image.maigesActMod Man page Source code
image.maigesActNet Man page Source code
image.maigesRaw Man page Source code
image.maigesRelNetB Man page Source code
image.maigesRelNetM Man page Source code
kmeansM Man page Source code
kmeansMde Man page Source code
loadData Man page Source code
maiges Man page
maiges-class Man page
maigesANOVA Man page
maigesANOVA-class Man page
maigesActMod Man page
maigesActMod-class Man page
maigesActNet Man page
maigesActNet-class Man page
maigesClass Man page
maigesClass-class Man page
maigesDE Man page
maigesDE-class Man page
maigesDEcluster Man page
maigesDEcluster-class Man page
maigesPreRaw Man page
maigesPreRaw-class Man page
maigesRaw Man page
maigesRaw-class Man page
maigesRelNetB Man page
maigesRelNetB-class Man page
maigesRelNetM Man page
maigesRelNetM-class Man page
normLoc Man page Source code
normOLIN Man page Source code
normRepLoess Man page Source code
normScaleLimma Man page Source code
normScaleMarray Man page Source code
plot Man page
plot.maiges Man page Source code
plot.maigesANOVA Man page
plot.maigesActMod Man page Source code
plot.maigesActNet Man page Source code
plot.maigesClass Man page Source code
plot.maigesDE Man page Source code
plot.maigesDEcluster Man page Source code
plot.maigesRaw Man page Source code
plot.maigesRelNetB Man page Source code
plot.maigesRelNetM Man page Source code
plotGenePair Man page Source code
print Man page
print.maiges Man page Source code
print.maigesANOVA Man page Source code
print.maigesActMod Man page Source code
print.maigesActNet Man page Source code
print.maigesClass Man page Source code
print.maigesDE Man page Source code
print.maigesDEcluster Man page
print.maigesPreRaw Man page Source code
print.maigesRaw Man page Source code
print.maigesRelNetB Man page Source code
print.maigesRelNetM Man page Source code
relNet2TGF Man page Source code
relNet2TGF.maigesRelNetB Man page Source code
relNet2TGF.maigesRelNetM Man page Source code
relNetworkB Man page Source code
relNetworkM Man page Source code
robustCorr Man page Source code
selSpots Man page Source code
show Man page
show,maiges-method Man page
show,maigesANOVA-method Man page
show,maigesActMod-method Man page
show,maigesActNet-method Man page
show,maigesClass-method Man page
show,maigesDE-method Man page
show,maigesDEcluster-method Man page
show,maigesPreRaw-method Man page
show,maigesRaw-method Man page
show,maigesRelNetB-method Man page
show,maigesRelNetM-method Man page
somM Man page Source code
somMde Man page Source code
summarizeReplicates Man page Source code
summary Man page
summary.maiges Man page Source code
summary.maigesANOVA Man page Source code
summary.maigesActMod Man page Source code
summary.maigesActNet Man page Source code
summary.maigesClass Man page Source code
summary.maigesDE Man page Source code
summary.maigesDEcluster Man page
summary.maigesPreRaw Man page Source code
summary.maigesRaw Man page Source code
summary.maigesRelNetB Man page Source code
summary.maigesRelNetM Man page Source code
tableClass Man page Source code
tablesDE Man page Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/MI.R
R/activeMod.R
R/activeModScoreHTML.R
R/activeNet.R
R/activeNetScoreHTML.R
R/addGeneGrps.R
R/addPaths.R
R/bootstrapCor.R
R/bootstrapMI.R
R/bootstrapT.R
R/boxplot-methods.R
R/calcA-methods.R
R/calcW-methods.R
R/classifyKNN.R
R/classifyKNNsc.R
R/classifyLDA.R
R/classifyLDAsc.R
R/classifySVM.R
R/classifySVMsc.R
R/coerce-methods.R
R/colors.R
R/compCorr.R
R/contrastsFitM.R
R/createMaigesRaw.R
R/createTDMS.R
R/deGenes2by2BootT.R
R/deGenes2by2Ttest.R
R/deGenes2by2Wilcox.R
R/deGenesANOVA.R
R/designANOVA.R
R/dim-methods.R
R/getLabels-methods.R
R/heatmapsM.R
R/hierM.R
R/hierMde.R
R/image-methods.R
R/indexing-methods.R
R/kmeansM.R
R/kmeansMde.R
R/loadData.R
R/normLoc.R
R/normOLIN.R
R/normRepLoess.R
R/normScaleLimma.R
R/normScaleMarray.R
R/plot-methods.R
R/plotGenePair.R
R/print-methods.R
R/relNet2TGF.R
R/relNetworkB.R
R/relNetworkM.R
R/robustCorr.R
R/selSpots.R
R/show-methods.R
R/somM.R
R/somMde.R
R/summarizeReplicates.R
R/summary-methods.R
R/tableClass.R
R/tablesDE.R
build
build/vignette.rds
data
data/gastro.RData
inst
inst/doc
inst/doc/maigesPack_tutorial.R
inst/doc/maigesPack_tutorial.Rnw
inst/doc/maigesPack_tutorial.pdf
man
man/MI.Rd
man/activeMod.Rd
man/activeModScoreHTML.Rd
man/activeNet.Rd
man/activeNetScoreHTML.Rd
man/addGeneGrps.Rd
man/addPaths.Rd
man/bootstrapCor.Rd
man/bootstrapMI.Rd
man/bootstrapT.Rd
man/boxplot-methods.Rd
man/bracketMethods.Rd
man/calcA.Rd
man/calcW.Rd
man/classifyKNN.Rd
man/classifyKNNsc.Rd
man/classifyLDA.Rd
man/classifyLDAsc.Rd
man/classifySVM.Rd
man/classifySVMsc.Rd
man/coerce-methods.Rd
man/compCorr.Rd
man/contrastsFitM.Rd
man/createMaigesRaw.Rd
man/createTDMS.Rd
man/deGenes2by2BootT.Rd
man/deGenes2by2Ttest.Rd
man/deGenes2by2Wilcox.Rd
man/deGenesANOVA.Rd
man/designANOVA.Rd
man/dim-methods.Rd
man/gastro.Rd
man/getLabels.Rd
man/heatmapsM.Rd
man/hierM.Rd
man/hierMde.Rd
man/image-methods.Rd
man/kmeansM.Rd
man/kmeansMde.Rd
man/loadData.Rd
man/maiges-class.Rd
man/maigesANOVA-class.Rd
man/maigesActMod-class.Rd
man/maigesActNet-class.Rd
man/maigesClass-class.Rd
man/maigesDE-class.Rd
man/maigesDEcluster-class.Rd
man/maigesPreRaw-class.Rd
man/maigesRaw-class.Rd
man/maigesRelNetB-class.Rd
man/maigesRelNetM-class.Rd
man/normLoc.Rd
man/normOLIN.Rd
man/normRepLoess.Rd
man/normScaleLimma.Rd
man/normScaleMarray.Rd
man/plot-methods.Rd
man/plotGenePair.Rd
man/print-methods.Rd
man/relNet2TGF.Rd
man/relNetworkB.Rd
man/relNetworkM.Rd
man/robustCorr.Rd
man/selSpots.Rd
man/show-methods.Rd
man/somM.Rd
man/somMde.Rd
man/summarizeReplicates.Rd
man/summary-methods.Rd
man/tableClass.Rd
man/tablesDE.Rd
src
src/Minfo.c
src/bootstrapT.c
src/register.c
src/robustCorr.c
src/stats.c
src/stats.h
vignettes
vignettes/gastro
vignettes/gastro/geneMap.txt
vignettes/gastro/load_gastro.conf
vignettes/gastro/sampleFile.txt
vignettes/maigesPack.graphml
vignettes/maigesPack.png
vignettes/maigesPack_tutorial.Rnw
maigesPack documentation built on May 20, 2017, 9:29 p.m.