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

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

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>
Date of publicationNone
MaintainerGustavo H. Esteves <gesteves@gmail.com>
LicenseGPL (>= 2)
Version1.38.0
http://www.maiges.org/en/software/

View on Bioconductor

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

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

Files

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

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