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

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

Author
Gustavo 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 publication
None
Maintainer
Gustavo H. Esteves <gesteves@gmail.com>
License
GPL (>= 2)
Version
1.38.0
URLs

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

Files in this package

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