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


[Package List] [Top]

Documentation for package ‘maigesPack’ version 1.6.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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,maiges,MAList-method Coerce a maiges object to classes defined by packages limma and marray
as,maiges,marrayNorm-method Coerce a maiges object to classes defined by packages limma and marray
as,maigesRaw,marrayRaw-method Coerce a maiges object to classes defined by packages limma and marray
as,maigesRaw,RGList-method Coerce a maiges object to classes defined by packages limma and marray
as,MAList,maiges-method Coerce a maiges object to classes defined by packages limma and marray
as,marrayNorm,maiges-method Coerce a maiges object to classes defined by packages limma and marray
as,marrayRaw,maigesRaw-method Coerce a maiges object to classes defined by packages limma and marray
as,RGList,maigesRaw-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

-- C --

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 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,maiges,MAList-method Coerce a maiges object to classes defined by packages limma and marray
coerce,maiges,marrayNorm-method Coerce a maiges object to classes defined by packages limma and marray
coerce,maigesRaw,marrayRaw-method Coerce a maiges object to classes defined by packages limma and marray
coerce,maigesRaw,RGList-method Coerce a maiges object to classes defined by packages limma and marray
coerce,MAList,maiges-method Coerce a maiges object to classes defined by packages limma and marray
coerce,marrayNorm,maiges-method Coerce a maiges object to classes defined by packages limma and marray
coerce,marrayRaw,maigesRaw-method Coerce a maiges object to classes defined by packages limma and marray
coerce,RGList,maigesRaw-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
getLabels 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

-- 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
plotGenePair Scatter plots for pair of genes
print Method to print a nice visualisation of the objects defined in this package

-- R --

relNet2TGF 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,maiges-method Show a nice visualisation of the objects defined in this package
show,maigesActMod-method Show a nice visualisation of the objects defined in this package
show,maigesActNet-method Show a nice visualisation of the objects defined in this package
show,maigesANOVA-method Show a nice visualisation of the objects defined in this package
show,maigesClass-method Show a nice visualisation of the objects defined in this package
show,maigesDE-method Show a nice visualisation of the objects defined in this package
show,maigesDEcluster-method Show a nice visualisation of the objects defined in this package
show,maigesPreRaw-method Show a nice visualisation of the objects defined in this package
show,maigesRaw-method Show a nice visualisation of the objects defined in this package
show,maigesRelNetB-method Show a nice visualisation of the objects defined in this package
show,maigesRelNetM-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

-- 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
[,maiges-method Sub-setting methods for maiges objects
[,maigesANOVA-method Sub-setting methods for maiges objects
[,maigesPreRaw-method Sub-setting methods for maiges objects
[,maigesRaw-method Sub-setting methods for maiges objects