Package: made4 1.81.0

Aedin Culhane

made4: Multivariate analysis of microarray data using ADE4

Multivariate data analysis and graphical display of microarray data. Functions include for supervised dimension reduction (between group analysis) and joint dimension reduction of 2 datasets (coinertia analysis). It contains functions that require R package ade4.

Authors:Aedin Culhane

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made4/json (API)

# Install 'made4' in R:
install.packages('made4', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • NCI60 - Microarray gene expression profiles of the NCI 60 cell lines
  • khan - Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.

On BioConductor:made4-1.79.0(bioc 3.20)made4-1.78.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

clusteringclassificationdimensionreductionprincipalcomponenttranscriptomicsmultiplecomparisongeneexpressionsequencingmicroarray

6.02 score 2 packages 87 scripts 610 downloads 86 mentions 32 exports 41 dependencies

Last updated 23 days agofrom:654689ebd0. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:asDataFramebet.coinertiabetween.graphbgabga.jackknifebga.supplciacommonMapcomparelistsdo3dgetcolgraph1Dheatplothtml3DisDataFrameordoverviewplot.bgaplot.ciaplot.ordplot.supplplotarraysplotgenesprettyDendprint.comparelistsrandomiserrotate3ds.groupss.varsumstatssuppltopgenes

Dependencies:abindade4askpassBiobaseBiocGenericsbitopscaToolscrayoncurlDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangesgplotsgtoolshttrIRangesjsonliteKernSmoothlatticeMASSMatrixMatrixGenericsmatrixStatsmimeopensslpixmapR6RColorBrewerRcppRcppArmadilloS4ArraysS4Vectorsscatterplot3dspSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

Introduction to Multivariate Analysis of Gene Expression Data using MADE4

Aedin Culhane

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2020-10-14
Started: 2020-10-13

Readme and manuals

Help Manual

Help pageTopics
Between class coinertia analysisbet.coinertia
Plot 1D graph of results from between group analysisbetween.graph
Between group analysisbga plot.bga
Jackknife between group analysisbga.jackknife
Between group analysis with supplementary data projectionbga.suppl
Coinertia analysis: Explore the covariance between two datasetscia plot.cia
Plot highlights common points between two 1D plots (biparitite)commonMap
Return the intersect, difference and union between 2 vectorscomparelists print.comparelists
Generate 3D graph(s) using scatterplot3ddo3d rotate3d
Specialised colour palette with set of 21 maximally contrasting coloursgetcol
Plot 1D graph of axis from multivariate analysisgraph1D
Draws heatmap with dendrograms.heatplot
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 Rasmolhtml3D
Converts microarray input data into a data frame suitable for analysis in ADE4.isDataFrame
Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.khan
Microarray gene expression profiles of the NCI 60 cell linesNCI60
Ordinationord plot.ord
Draw boxplot, histogram and hierarchical tree of gene expression dataoverview
Graph xy plot of variable (array) projections from ordination, between group analysis or coinertia analysis.plotarrays
Graph xy plot of variable (gene) projections from PCA or COA. Only label variables at ends of axesplotgenes
Draw hierarchical tree of gene expression data with a colorbar for numerous class vectorsprettyDend
Randomly reassign training and test samplesrandomiser
Summary statistics on xy co-ordinates, returns the slopes and distance from origin of each co-ordinate.sumstats
Projection of supplementary data onto axes from a between group analysisplot.suppl suppl
Topgenes, returns a list of variables at the ends (positive, negative or both) of an axistopgenes