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made4 (version 1.46.0)

Multivariate analysis of microarray data using ADE4

Description

Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.

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Version

Version

1.46.0

License

Artistic-2.0

Maintainer

Aedin Culhane

Last Published

February 15th, 2017

Functions in made4 (1.46.0)

checkfac

Check factor
topgenes

Topgenes, returns a list of variables at the ends (positive, negative or both) of an axis
plotarrays

Graph xy plot of variable (array) projections from ordination, between group analysis or coinertia analysis.
overview

Draw boxplot, histogram and hierarchical tree of gene expression data
s.var

Draw xy plots of results of multivariate analysis
sumstats

Summary statistics on xy co-ordinates, returns the slopes and distance from origin of each co-ordinate.
genes

Returns an index of the top N variables at the ends of the x and y axes
jmol3D

Produce web graph of 3D graph that can be viewed using Jmol in web browser
graph1D

Plot 1D graph of axis from multivariate analysis
dudi.rwcoa

Row weighted Correspondence Analysis
bga

Between group analysis
ord

Ordination
comparelists

Return the intersect, difference and union between 2 vectors
cia

Coinertia analysis: Explore the covariance between two datasets
forrwcoa

Row weighted Correspondence Analysis
html3D

Produce web page with a 3D graph that can be viewed using Chime web browser plug-in, and/or a pdb file that can be viewed using Rasmol
heatplot

Draws heatmap with dendrograms.
khan

Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
NCI60

Microarray gene expression profiles of the NCI 60 cell lines
bga.jackknife

Jackknife between group analysis
bet.coinertia

Between class coinertia analysis
array2ade4

Converts microarray input data into a data frame suitable for analysis in ADE4.
commonMap

Highlight common points between two 1D plots
getdata

Check dataset
suppl

Projection of supplementary data onto axes from a between group analysis
plotgenes

Graph xy plot of variable (gene) projections from PCA or COA. Only label variables at ends of axes
between.graph

Plot 1D graph of results from between group analysis
randomiser

Randomly reassign training and test samples
bga.suppl

Between group analysis with supplementary data projection
genes1d

genes1d: list top N variables on one axis. Lists the maximum and minimum values in a column of a data.frame
getcol

Specialised colour palette with set of 21 maximally contrasting colours
do3d

Generate 3D graph(s) using scatterplot3d
chime3D

Produce web graph of 3D graph that can be viewed using Chime web browser plug-in from a pdb file
prettyDend

Draw hierarchical tree of gene expression data with a colorbar for numerous class vectors