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

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

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