CAFE: Chromosmal Aberrations Finder in Expression data
Version 1.12.0

Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input

Browse man pages Browse package API and functions Browse package files

AuthorSander Bollen
Bioconductor views GeneExpression GeneSetEnrichment Microarray OneChannel
Date of publicationNone
MaintainerSander Bollen <sander.h.bollen@gmail.com>
LicenseGPL-3
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CAFE")

Man pages

armStats: Find aberrations with chromosome arm resolution
bandStats: Find aberrations with cytoband resolution
CAFE: CAFE data set
CAFE-package: Chromosomal Aberrations Finder in Expression data
chromosomeStats: Find aberrations with whole-chromosome resolution
cliSubset: Subset data with a CLI
discontPlot: Plot with discontinuous smoother
discontSmooth: A discontinuous smoother
facetPlot: Plot all chromosomes horizontally next to each other
fisher.method: Combines pvalues by using Fisher's method
guiSubset: Subset data with a GUI
ProcessCels: Processing CEL files
rawPlot: Plot without any smoother
slidPlot: Plot with sliding average smoother
slidSmooth: A moving average smoother

Functions

Armchisqr Source code
ArmfisherExact Source code
CAFE Man page
CAFE-package Man page
CAFE_data Man page
FindBestPartition Source code
ProcessCels Man page Source code
allBandsOnChrom Source code
allBandsOnChromChi Source code
armStats Man page Source code
bandStats Man page Source code
chisqr Source code
chromosomeStats Man page Source code
cliSubset Man page Source code
discontPlot Man page Source code
discontSmooth Man page Source code
facetPlot Man page Source code
fisher.method Man page Source code
fisherExact Source code
guiSubset Man page Source code
makeArmContingency Source code
makeBandContingency Source code
makeContingency Source code
makelevels Source code
mu Source code
rawPlot Man page Source code
segmentationFromPartition Source code
slidPlot Man page Source code
slidSmooth Man page Source code
slidWithGaps Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/chromosomeStats.R
R/discontPlot.R
R/facetPlot.R
R/microProcess-improve.R
R/rawPlot.R
R/selectSamples.R
R/slidPlot.R
build
build/vignette.rds
data
data/CAFE_data.RData
data/datalist
inst
inst/doc
inst/doc/CAFE-manual.R
inst/doc/CAFE-manual.Rnw
inst/doc/CAFE-manual.pdf
inst/unitTests
inst/unitTests/test_CAFE_ProcessCels.R
inst/unitTests/test_CAFE_armStats.R
inst/unitTests/test_CAFE_bandStats.R
inst/unitTests/test_CAFE_chromosomeStats.R
inst/unitTests/test_CAFE_cliSubset.R
inst/unitTests/test_CAFE_discontPlot.R
inst/unitTests/test_CAFE_discontSmooth.R
inst/unitTests/test_CAFE_facetPlot.R
inst/unitTests/test_CAFE_guiSubset.R
inst/unitTests/test_CAFE_rawPlot.R
inst/unitTests/test_CAFE_slidPlot.R
inst/unitTests/test_CAFE_slidSmooth.R
man
man/CAFE-package.Rd
man/CAFE.Rd
man/ProcessCels.Rd
man/armStats.Rd
man/bandStats.Rd
man/chromosomeStats.Rd
man/cliSubset.Rd
man/discontPlot.Rd
man/discontSmooth.Rd
man/facetPlot.Rd
man/fisher.method.Rd
man/guiSubset.Rd
man/rawPlot.Rd
man/slidPlot.Rd
man/slidSmooth.Rd
tests
tests/runTests.R
vignettes
vignettes/CAFE-manual.Rnw
vignettes/manual.bib
vignettes/simple.png
CAFE documentation built on May 20, 2017, 10:12 p.m.