KCsmart: Multi sample aCGH analysis package using kernel convolution

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Multi sample aCGH analysis package using kernel convolution

Author
Jorma de Ronde, Christiaan Klijn, Arno Velds
Date of publication
None
Maintainer
Jorma de Ronde <j.d.ronde@nki.nl>
License
GPL-3
Version
2.32.0

View on Bioconductor

Man pages

calcSpm
KCsmart wrapper
calcSpmCollection
KCsmart Comparative wrapper
compareSpmCollection
KCsmart Comparative calculate null distribution
compKc-class
KC smart comparative
compKcSigRegions-class
KC smart comparative
findSigLevelFdr
This function has not been properly implemented yet
findSigLevelTrad
Find significance level
getSigRegionsCompKC
KCsmart Comparative calculate the signficant regions
getSigSegments
Retrieve the significantly gained and lost regions including...
hsMirrorLocs
Mirror locations of the human genome
hsSampleData
Homo Sapiens artificial cgh data set
idPoints
Identify points in sample point matrix plot
KCData-class
Internal class "KCData"
KcghData-class
Class "KcghData"
KcghDataMirror-class
Class "KcghDataMirror"
KcghDataSplit-class
Class "KcghDataSplit"
KcghDataSum-class
Class "KcghDataSum"
KCsmart-package
KCsmart
mmMirrorLocs
Mirror locations of the mouse genome
plot
Plot a sample point matrix
plotScaleSpace
Plot multiple significant regions in one figure
probeAnnotation-class
Class "probeAnnotation"
samplePointMatrix-class
Sample point matrix
sigSegments-class
Significant segments
spmCollection-class
Sample point matrix collection
write.table
Write summary of the significant regions to a table

Files in this package

KCsmart/DESCRIPTION
KCsmart/NAMESPACE
KCsmart/R
KCsmart/R/AllClasses.R
KCsmart/R/KC.R
KCsmart/R/access-methods.R
KCsmart/R/length-methods.R
KCsmart/R/plot-methods.R
KCsmart/R/show-methods.R
KCsmart/R/sort-methods.R
KCsmart/R/unlist-methods.R
KCsmart/R/write.table-methods.R
KCsmart/build
KCsmart/build/vignette.rds
KCsmart/data
KCsmart/data/hsMirrorLocs.rda
KCsmart/data/hsSampleData.rda
KCsmart/data/mmMirrorLocs.rda
KCsmart/inst
KCsmart/inst/doc
KCsmart/inst/doc/KCS.R
KCsmart/inst/doc/KCS.Rnw
KCsmart/inst/doc/KCS.pdf
KCsmart/man
KCsmart/man/KCData-class.Rd
KCsmart/man/KCsmart-package.Rd
KCsmart/man/KcghData-class.Rd
KCsmart/man/KcghDataMirror-class.Rd
KCsmart/man/KcghDataSplit-class.Rd
KCsmart/man/KcghDataSum-class.Rd
KCsmart/man/calcSpm.Rd
KCsmart/man/calcSpmCollection.Rd
KCsmart/man/compKc-class.Rd
KCsmart/man/compKcSigRegions-class.Rd
KCsmart/man/compareSpmCollection.Rd
KCsmart/man/findSigLevelFdr.Rd
KCsmart/man/findSigLevelTrad.Rd
KCsmart/man/getSigRegionsCompKC.Rd
KCsmart/man/getSigSegments.Rd
KCsmart/man/hsMirrorLocs.Rd
KCsmart/man/hsSampleData.Rd
KCsmart/man/idPoints.Rd
KCsmart/man/mmMirrorLocs.Rd
KCsmart/man/plot.Rd
KCsmart/man/plotScaleSpace.Rd
KCsmart/man/probeAnnotation-class.Rd
KCsmart/man/samplePointMatrix-class.Rd
KCsmart/man/sigSegments-class.Rd
KCsmart/man/spmCollection-class.Rd
KCsmart/man/write.table.Rd
KCsmart/vignettes
KCsmart/vignettes/KCS.Rnw