macat: MicroArray Chromosome Analysis Tool
Version 1.50.0

This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'.

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AuthorBenjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian Schmeier, Joern Toedling
Bioconductor views DifferentialExpression Microarray Visualization
Date of publicationNone
MaintainerJoern Toedling <jtoedling@yahoo.de>
LicenseArtistic-2.0
Version1.50.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("macat")

Man pages

buildMACAT: Create MACAT list from objects in workspace
compute_sliding: Compute and plot smoothing of expression values or scores...
discreteKernelize: Discretize and smooth expression values
discretize: Discretize expression values
discretizeAll: Discretize complete expression matrix
discretize_tscores: Discretize regularized t-scores
evalScoring: Score differential expression, assess significance, and...
evaluateParameters: Evaluate Performance of Kernel Parameters by Cross-validation
get_results: Access results of 'evalScoring'
html: HTML functions for MACAT.
kernelize: Smooth expression values or scores
kernelizeAll: Smooth expression data for all chromosomes
kernelizeToPython: Smooth expression values and write to file
kernels: various kernel functions for computations in MACAT
loaddatapkg: Load data package
macat-internal: Auxiliary Functions for Computations in MACAT
plot_MACATevalScoring: Plot function for MACATevalScoring objects.
preprocessedLoader: Read in data and produce MACAT list
pythondata: Flat file format
scoring: Compute (regularized) t-scores for gene expression data
stjd: Subset Microarray Data from St.Jude Children Research...

Functions

Loader Man page
MACATData Man page
MACATinput Man page
basePairDistance Man page Source code
buildMACAT Man page Source code
compare.gammas Man page Source code
compute.sliding Man page Source code
crossvalParam Man page Source code
demo.part Man page Source code
discreteKernelize Man page Source code
discretize Man page Source code
discretize.tscores Man page Source code
discretizeAll Man page Source code
discretizeAllClasses.tscores Man page Source code
discretizeChromosome Man page Source code
discretizeOne Man page Source code
evalParams Man page Source code
evalScoring Man page Source code
evaluateParameters Man page Source code
fitkernelparams Man page Source code
getExpression.MACATData Man page Source code
getExpressionByChromosome.MACATData Man page Source code
getExpressionByClass.MACATData Man page Source code
getExpressionByProbeset.MACATData Man page Source code
getFromDb Man page Source code
getHtml Man page Source code
getResults Man page Source code
getsteps Man page Source code
kNN Man page Source code
kernelize Man page Source code
kernelizeAll Man page Source code
kernelizeToPython Man page Source code
kernelmatrix Man page Source code
kernels Man page
loaddatapkg Man page Source code
maxDistances Man page Source code
myhtml Man page Source code
onAttach Source code
onLoad Source code
onUnload Source code
pair.distances Man page Source code
plot.MACATevP Man page Source code
plot.MACATevalScoring Man page Source code
plotSliding Man page Source code
preprocessedLoader Man page Source code
pydata Man page
pythondata Man page
rawDataToPython Man page Source code
rbf Man page Source code
saveForPython Man page Source code
scoring Man page Source code
slidingAverageAt Man page
squaredDist Man page Source code
stjd Man page
toPython Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/SlidingAverage.R
R/crossvalFunctions.R
R/demo.part.R
R/discretescoring.R
R/evalScoring.R
R/html.R
R/loaddatapkg.R
R/preprocessedLoader.R
R/scoring.R
R/zzz.R
build
build/vignette.rds
data
data/stjd.RData
demo
demo/00Index
demo/macatdemo.R
inst
inst/CITATION
inst/doc
inst/doc/macat.R
inst/doc/macat.Rnw
inst/doc/macat.pdf
man
man/buildMACAT.Rd
man/compute_sliding.Rd
man/discreteKernelize.Rd
man/discretize.Rd
man/discretizeAll.Rd
man/discretize_tscores.Rd
man/evalScoring.Rd
man/evaluateParameters.Rd
man/get_results.Rd
man/html.Rd
man/kernelize.Rd
man/kernelizeAll.Rd
man/kernelizeToPython.Rd
man/kernels.Rd
man/loaddatapkg.Rd
man/macat-internal.Rd
man/plot_MACATevalScoring.Rd
man/preprocessedLoader.Rd
man/pythondata.Rd
man/scoring.Rd
man/stjd.Rd
vignettes
vignettes/Makefile
vignettes/Slidingchrom6s3.pdf
vignettes/chrom6T.pdf
vignettes/chrom6TkNN.pdf
vignettes/evalkNN6.pdf
vignettes/macat.Rnw
macat documentation built on May 20, 2017, 9:43 p.m.