Multi sample aCGH analysis package using kernel convolution

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Documentation for package ‘KCsmart’ version 2.32.0

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KCsmart-package KCsmart
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 the corresponding, original probes
hsMirrorLocs Mirror locations of the human genome
hsSampleData Homo Sapiens artificial cgh data set
idPoints Identify points in sample point matrix plot
initialize-method Class "KcghData"
initialize-method Class "KcghDataMirror"
initialize-method Class "KcghDataSplit"
initialize-method Class "KcghDataSum"
initialize-method KC smart comparative
initialize-method Class "probeAnnotation"
KCData-class Internal class "KCData"
KcghData-class Class "KcghData"
KcghDataMirror-class Class "KcghDataMirror"
KcghDataSplit-class Class "KcghDataSplit"
KcghDataSum-class Class "KcghDataSum"
KCsmart KCsmart
length-method Internal class "KCData"
mmMirrorLocs Mirror locations of the mouse genome
plot Plot a sample point matrix
plot-method KC smart comparative
plot-method Plot a sample point matrix
plotScaleSpace Plot multiple significant regions in one figure
probeAnnotation-class Class "probeAnnotation"
samplePointMatrix-class Sample point matrix
show-method KC smart comparative
show-method KC smart comparative
show-method Sample point matrix
show-method Significant segments
show-method Sample point matrix collection
sigSegments-class Significant segments
sort-method Class "KcghData"
sort-method Class "KcghDataSum"
spmCollection-class Sample point matrix collection
unlist-method Internal class "KCData"
write.table Write summary of the significant regions to a table
write.table-method Write summary of the significant regions to a table
[-method Class "probeAnnotation"
[[-method Internal class "KCData"
[[<--method Internal class "KCData"