Entry: NCI60
Aliases: NCI60
Keywords: datasets
Description: Microarray gene expression profiles of the NCI 60 cell lines
URL: ../../../library/made4/html/NCI60.html

Entry: array2ade4
Aliases: array2ade4
Keywords: manip
Description: Converts microarray input data into a data frame suitable for analysis in ADE4.
URL: ../../../library/made4/html/array2ade4.html

Entry: bet.coinertia
Aliases: bet.coinertia
Keywords: multivariate manip
Description: Between class coinertia analysis
URL: ../../../library/made4/html/bet.coinertia.html

Entry: between.graph
Aliases: between.graph
Keywords: multivariate hplot
Description: Plot 1D graph of results from between group analysis
URL: ../../../library/made4/html/between.graph.html

Entry: bga
Aliases: bga plot.bga
Keywords: manip multivariate
Description: Between group analysis
URL: ../../../library/made4/html/bga.html

Entry: bga.jackknife
Aliases: bga.jackknife
Keywords: manip multivariate
Description: Jackknife between group analysis
URL: ../../../library/made4/html/bga.jackknife.html

Entry: bga.suppl
Aliases: bga.suppl
Keywords: manip multivariate
Description: Between group analysis with supplementary data projection
URL: ../../../library/made4/html/bga.suppl.html

Entry: checkfac
Aliases: checkfac
Keywords: internal
Description: Check factor
URL: ../../../library/made4/html/checkfac.html

Entry: chime3D
Aliases: chime3D
Keywords: internal
Description: Produce web graph of 3D graph that can be viewed using Chime web browser plug-in from a pdb file
URL: ../../../library/made4/html/chime3D.html

Entry: cia
Aliases: cia plot.cia
Keywords: multivariate hplot
Description: Coinertia analysis: Explore the covariance between two datasets
URL: ../../../library/made4/html/cia.html

Entry: commonMap
Aliases: commonMap
Keywords: multivariate hplot
Description: Highlight common points between two 1D plots
URL: ../../../library/made4/html/commonMap.html

Entry: comparelists
Aliases: comparelists print.comparelists
Keywords: manip
Description: Return the intersect, difference and union between 2 vectors
URL: ../../../library/made4/html/comparelists.html

Entry: do3d
Aliases: do3d rotate3d
Keywords: hplot
Description: Generate 3D graph(s) using scatterplot3d
URL: ../../../library/made4/html/do3d.html

Entry: dudi.rwcoa
Aliases: dudi.rwcoa
Keywords: internal
Description: Row weighted Correspondence Analysis
URL: ../../../library/made4/html/dudi.rwcoa.html

Entry: forrwcoa
Aliases: forrwcoa
Keywords: internal
Description: Row weighted Correspondence Analysis
URL: ../../../library/made4/html/forrwcoa.html

Entry: genes
Aliases: genes
Keywords: internal
Description: Returns an index of the top N variables at the ends of the x and y axes
URL: ../../../library/made4/html/genes.html

Entry: genes1d
Aliases: genes1d
Keywords: internal
Description: genes1d: list top N variables on one axis. Lists the maximum and minimum values in a column of a data.frame
URL: ../../../library/made4/html/genes1d.html

Entry: getcol
Aliases: getcol
Keywords: color hplot
Description: Specialised colour palette with set of 21 maximally contrasting colours
URL: ../../../library/made4/html/getcol.html

Entry: getdata
Aliases: getdata
Keywords: internal
Description: Check dataset
URL: ../../../library/made4/html/getdata.html

Entry: graph1D
Aliases: graph1D
Keywords: hplot manip
Description: Plot 1D graph of axis from multivariate analysis
URL: ../../../library/made4/html/graph1D.html

Entry: heatplot
Aliases: heatplot
Keywords: hplot manip
Description: Draws heatmap with dendrograms.
URL: ../../../library/made4/html/heatplot.html

Entry: html3D
Aliases: html3D
Keywords: hplot
Description: 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
URL: ../../../library/made4/html/html3D.html

Entry: jmol3D
Aliases: jmol3D
Keywords: internal
Description: Produce web graph of 3D graph that can be viewed using Jmol in web browser
URL: ../../../library/made4/html/jmol3D.html

Entry: khan
Aliases: khan
Keywords: datasets
Description: Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
URL: ../../../library/made4/html/khan.html

Entry: ord
Aliases: ord plot.ord
Keywords: manip multivariate
Description: Ordination
URL: ../../../library/made4/html/ord.html

Entry: overview
Aliases: overview
Keywords: hplot manip
Description: Draw boxplot, histogram and hierarchical tree of gene expression data
URL: ../../../library/made4/html/overview.html

Entry: plotarrays
Aliases: plotarrays
Keywords: multivariate hplot
Description: Graph xy plot of variable (array) projections from ordination, between group analysis or coinertia analysis.
URL: ../../../library/made4/html/plotarrays.html

Entry: plotgenes
Aliases: plotgenes
Keywords: multivariate hplot
Description: Graph xy plot of variable (gene) projections from PCA or COA. Only label variables at ends of axes
URL: ../../../library/made4/html/plotgenes.html

Entry: pretty.dend
Aliases: pretty.dend
Keywords: hplot manip
Description: Draw hierarchical tree of gene expression data with a colorbar for numerous class vectors
URL: ../../../library/made4/html/pretty.dend.html

Entry: randomiser
Aliases: randomiser
Keywords: manip
Description: Randomly reassign training and test samples
URL: ../../../library/made4/html/randomiser.html

Entry: s.var
Aliases: s.var s.groups s.match.col
Keywords: multivariate internal
Description: Draw xy plots of results of multivariate analysis
URL: ../../../library/made4/html/s.var.html

Entry: sumstats
Aliases: sumstats
Keywords: manip
Description: Summary statistics on xy co-ordinates, returns the slopes and distance from origin of each co-ordinate.
URL: ../../../library/made4/html/sumstats.html

Entry: suppl
Aliases: suppl plot.suppl
Keywords: manip multivariate
Description: Projection of supplementary data onto axes from a between group analysis
URL: ../../../library/made4/html/suppl.html

Entry: topgenes
Aliases: topgenes
Keywords: manip
Description: Topgenes, returns a list of variables at the ends (positive, negative or both) of an axis
URL: ../../../library/made4/html/topgenes.html
