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maigesPack (version 1.30.0)

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

Description

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

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Version

Version

1.30.0

License

GPL (>= 2)

Maintainer

Gustavo H Esteves

Last Published

February 15th, 2017

Functions in maigesPack (1.30.0)

boxplot

Method boxplot for objects defined in this package
compCorr

Compute correlation differences and their p-values
contrastsFitM

Compute Contrasts from Linear Model Fit
getLabels

Method getLabels to pick gene and sample labels
gastro

Gastro-esophagic dataset
maigesANOVA-class

maigesANOVA class, extend maiges class to fit ANOVA models
maigesClass-class

maigesClass class, store results of discrimination (or classification) analysis
bootstrapT

Calculate bootstrap p-values for t statistics
MI

Calculate Mutual Information
normLoc

Normalise a cDNA Microarray Object
tableClass

Save HTML or CSV tables of good classifiers (cliques)
summary

Method summary for the object from this package
bootstrapCor

Calculate bootstrap p-values for correlation measures
addGeneGrps

Function to load gene groups into maigesPreRaw object
addPaths

Function to load gene pathways into maigesPreRaw object
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
kmeansM

Function to do k-means cluster analysis
kmeansMde

Function to do k-means cluster analysis
maigesRelNetB-class

maigesRelNetB class, store results of relevance network analysis (Butte's method)
maigesRelNetM-class

maigesRelNetM class, store results of relevance network analysis (comparing two sample types)
normScaleLimma

Scale adjust a cDNA Microarray Object
bootstrapMI

Calculate bootstrap p-values for mutual information (MI) measures
classifyKNNsc

Function to do discrimination analysis, by the search and choose method
classifyLDA

Function to do discrimination analysis
createMaigesRaw

Function to create objects of class maigesRaw
maigesPreRaw-class

maigesPreRaw class, store pre raw microarray datasets
createTDMS

Create a tab delimited file for TIGR MeV
plot

Method plot for objects defined in this package
maigesRaw-class

maigesRaw class, store raw microarray datasets
relNetworkB

Relevance Network analysis
plotGenePair

Scatter plots for pair of genes
relNetworkM

Relevance Network analysis
tablesDE

Save HTML or CSV tables of differentially expressed genes
normScaleMarray

Scale adjust a cDNA Microarray Object
somMde

Function to do SOM cluster analysis
summarizeReplicates

Summarise microarray objects
activeMod

Functional classification of gene groups
activeModScoreHTML

Save HTML file with global gene scores from functional gene groups classification
classifyKNN

Function to do discrimination analysis
calcW

Method calcW to calculate W values
designANOVA

Function to construct design an contrasts matrices for ANOVA models
hierMde

Function to do hierarchical cluster analysis
dim

Retrieve the dimension of microarray objects
image

Method image for objects defined in this package
somM

Function to do SOM cluster analysis
show-method

Show a nice visualisation of the objects defined in this package
deGenes2by2Wilcox

Function to do differential expression analysis, comparing only two samples
classifySVM

Function to do discrimination analysis
classifyLDAsc

Function to do discrimination analysis, by the search and choose method
loadData

Load cDNA microarray data tables
deGenesANOVA

Function to do differential expression analysis, using ANOVA models
maiges-class

maiges class, store normalised microarray datasets
maigesDE-class

maigesDE class, store results of differential gene expression analysis
normOLIN

Normalise a cDNA Microarray Object
maigesDEcluster-class

maigesDEcluster class, store results of differential gene expression analysis
normRepLoess

Bootstrap of LOWESS normalisation
activeNet

Functional classification of gene networks
activeNetScoreHTML

Save HTML file with scores and p-values from functional gene networks classification
[-method

Sub-setting methods for maiges objects
calcA

Method calcA to calculate A values
deGenes2by2BootT

Function to do differential expression analysis, comparing only two samples
heatmapsM

Function to plot heatmaps separating groups generated by SOM or k-means
deGenes2by2Ttest

Function to do differential expression analysis, comparing only two samples
maigesActNet-class

maigesActNet class, store results of functional classification of gene networks
hierM

Function to do hierarchical cluster analysis
maigesActMod-class

maigesActMod class, store results of functional classification of gene groups
print

Method to print a nice visualisation of the objects defined in this package
relNet2TGF

Transform Relevance Network analysis in TGF output
robustCorr

Calculate a robust correlation value
selSpots

Select spots to use in normalisation