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


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Documentation for package ‘maigesPack’ version 1.58.0

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A B C D G H I K L M N P R S T misc

-- A --

activeMod Functional classification of gene groups
activeModScoreHTML Save HTML file with global gene scores from functional gene groups classification
activeNet Functional classification of gene networks
activeNetScoreHTML Save HTML file with scores and p-values from functional gene networks classification
addGeneGrps Function to load gene groups into maigesPreRaw object
addPaths Function to load gene pathways into maigesPreRaw object
as Coerce a maiges object to classes defined by packages limma and marray
as-method Coerce a maiges object to classes defined by packages limma and marray

-- B --

bootstrapCor Calculate bootstrap p-values for correlation measures
bootstrapMI Calculate bootstrap p-values for mutual information (MI) measures
bootstrapT Calculate bootstrap p-values for t statistics
boxplot Method boxplot for objects defined in this package
boxplot.maiges Method boxplot for objects defined in this package
boxplot.maigesANOVA Method boxplot for objects defined in this package
boxplot.maigesDEcluster Method boxplot for objects defined in this package
boxplot.maigesRaw Method boxplot for objects defined in this package

-- C --

calcA Method calcA to calculate A values
calcA.default Method calcA to calculate A values
calcA.maigesRaw Method calcA to calculate A values
calcW Method calcW to calculate W values
calcW.default Method calcW to calculate W values
calcW.maigesRaw Method calcW to calculate W values
classifyKNN Function to do discrimination analysis
classifyKNNsc Function to do discrimination analysis, by the search and choose method
classifyLDA Function to do discrimination analysis
classifyLDAsc Function to do discrimination analysis, by the search and choose method
classifySVM Function to do discrimination analysis
classifySVMsc Function to do discrimination analysis, by the search and choose method
coerce-method Coerce a maiges object to classes defined by packages limma and marray
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

-- D --

deGenes2by2BootT Function to do differential expression analysis, comparing only two samples
deGenes2by2Ttest Function to do differential expression analysis, comparing only two samples
deGenes2by2Wilcox Function to do differential expression analysis, comparing only two samples
deGenesANOVA Function to do differential expression analysis, using ANOVA models
designANOVA Function to construct design an contrasts matrices for ANOVA models
dim.maiges Retrieve the dimension of microarray objects
dim.maigesANOVA Retrieve the dimension of microarray objects
dim.maigesPreRaw Retrieve the dimension of microarray objects
dim.maigesRaw Retrieve the dimension of microarray objects

-- G --

gastro Gastro-esophagic dataset
gastro.norm Gastro-esophagic dataset
gastro.raw Gastro-esophagic dataset
gastro.raw2 Gastro-esophagic dataset
gastro.summ Gastro-esophagic dataset
getLabels Method getLabels to pick gene and sample labels
getLabels.default Method getLabels to pick gene and sample labels
getLabels.maigesDE Method getLabels to pick gene and sample labels
getLabels.maigesDEcluster Method getLabels to pick gene and sample labels
getLabels.MAList Method getLabels to pick gene and sample labels
getLabels.marrayNorm Method getLabels to pick gene and sample labels
getLabels.marrayRaw Method getLabels to pick gene and sample labels
getLabels.RGList Method getLabels to pick gene and sample labels

-- H --

heatmapsM Function to plot heatmaps separating groups generated by SOM or k-means
hierM Function to do hierarchical cluster analysis
hierMde Function to do hierarchical cluster analysis

-- I --

image Method image for objects defined in this package
image.maiges Method image for objects defined in this package
image.maigesActMod Method image for objects defined in this package
image.maigesActNet Method image for objects defined in this package
image.maigesANOVA Method image for objects defined in this package
image.maigesRaw Method image for objects defined in this package
image.maigesRelNetB Method image for objects defined in this package
image.maigesRelNetM Method image for objects defined in this package

-- K --

kmeansM Function to do k-means cluster analysis
kmeansMde Function to do k-means cluster analysis

-- L --

loadData Load cDNA microarray data tables

-- M --

maiges maiges class, store normalised microarray datasets
maiges-class maiges class, store normalised microarray datasets
maigesActMod maigesActMod class, store results of functional classification of gene groups
maigesActMod-class maigesActMod class, store results of functional classification of gene groups
maigesActNet maigesActNet class, store results of functional classification of gene networks
maigesActNet-class maigesActNet class, store results of functional classification of gene networks
maigesANOVA maigesANOVA class, extend maiges class to fit ANOVA models
maigesANOVA-class maigesANOVA class, extend maiges class to fit ANOVA models
maigesClass maigesClass class, store results of discrimination (or classification) analysis
maigesClass-class maigesClass class, store results of discrimination (or classification) analysis
maigesDE maigesDE class, store results of differential gene expression analysis
maigesDE-class maigesDE class, store results of differential gene expression analysis
maigesDEcluster maigesDEcluster class, store results of differential gene expression analysis
maigesDEcluster-class maigesDEcluster class, store results of differential gene expression analysis
maigesPreRaw maigesPreRaw class, store pre raw microarray datasets
maigesPreRaw-class maigesPreRaw class, store pre raw microarray datasets
maigesRaw maigesRaw class, store raw microarray datasets
maigesRaw-class maigesRaw class, store raw microarray datasets
maigesRelNetB maigesRelNetB class, store results of relevance network analysis (Butte's method)
maigesRelNetB-class maigesRelNetB class, store results of relevance network analysis (Butte's method)
maigesRelNetM maigesRelNetM class, store results of relevance network analysis (comparing two sample types)
maigesRelNetM-class maigesRelNetM class, store results of relevance network analysis (comparing two sample types)
MI Calculate Mutual Information

-- N --

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

-- P --

plot Method plot for objects defined in this package
plot.maiges Method plot for objects defined in this package
plot.maigesActMod Method plot for objects defined in this package
plot.maigesActNet Method plot for objects defined in this package
plot.maigesANOVA Method plot for objects defined in this package
plot.maigesClass Method plot for objects defined in this package
plot.maigesDE Method plot for objects defined in this package
plot.maigesDEcluster Method plot for objects defined in this package
plot.maigesRaw Method plot for objects defined in this package
plot.maigesRelNetB Method plot for objects defined in this package
plot.maigesRelNetM Method plot for objects defined in this package
plotGenePair Scatter plots for pair of genes
print Method to print a nice visualisation of the objects defined in this package
print.maiges Method to print a nice visualisation of the objects defined in this package
print.maigesActMod Method to print a nice visualisation of the objects defined in this package
print.maigesActNet Method to print a nice visualisation of the objects defined in this package
print.maigesANOVA Method to print a nice visualisation of the objects defined in this package
print.maigesClass Method to print a nice visualisation of the objects defined in this package
print.maigesDE Method to print a nice visualisation of the objects defined in this package
print.maigesDEcluster Method to print a nice visualisation of the objects defined in this package
print.maigesPreRaw Method to print a nice visualisation of the objects defined in this package
print.maigesRaw Method to print a nice visualisation of the objects defined in this package
print.maigesRelNetB Method to print a nice visualisation of the objects defined in this package
print.maigesRelNetM Method to print a nice visualisation of the objects defined in this package

-- R --

relNet2TGF Transform Relevance Network analysis in TGF output
relNet2TGF.maigesRelNetB Transform Relevance Network analysis in TGF output
relNet2TGF.maigesRelNetM Transform Relevance Network analysis in TGF output
relNetworkB Relevance Network analysis
relNetworkM Relevance Network analysis
robustCorr Calculate a robust correlation value

-- S --

selSpots Select spots to use in normalisation
show Show a nice visualisation of the objects defined in this package
show-method Show a nice visualisation of the objects defined in this package
somM Function to do SOM cluster analysis
somMde Function to do SOM cluster analysis
summarizeReplicates Summarise microarray objects
summary Method summary for the object from this package
summary.maiges Method summary for the object from this package
summary.maigesActMod Method summary for the object from this package
summary.maigesActNet Method summary for the object from this package
summary.maigesANOVA Method summary for the object from this package
summary.maigesClass Method summary for the object from this package
summary.maigesDE Method summary for the object from this package
summary.maigesDEcluster Method summary for the object from this package
summary.maigesPreRaw Method summary for the object from this package
summary.maigesRaw Method summary for the object from this package
summary.maigesRelNetB Method summary for the object from this package
summary.maigesRelNetM Method summary for the object from this package

-- T --

tableClass Save HTML or CSV tables of good classifiers (cliques)
tablesDE Save HTML or CSV tables of differentially expressed genes

-- misc --

[ Sub-setting methods for maiges objects
[-method Sub-setting methods for maiges objects