# Multi sample aCGH analysis package using kernel convolution

## Documentation for package ‘KCsmart’ version 2.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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,compKc-method | KC smart comparative
initialize,KcghData-method | Class "KcghData"
initialize,KcghDataMirror-method | Class "KcghDataMirror"
initialize,KcghDataSplit-method | Class "KcghDataSplit"
initialize,KcghDataSum-method | Class "KcghDataSum"
initialize,probeAnnotation-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,KCData-method | Internal class "KCData"
mmMirrorLocs | Mirror locations of the mouse genome
plot | Plot a sample point matrix
plot,compKc,missing-method | Plot a sample point matrix
plot,compKc-method | KC smart comparative
plot,samplePointMatrix,missing-method | Plot a sample point matrix
plot,scaleSpace,missing-method | Plot a sample point matrix
plotScaleSpace | Plot multiple significant regions in one figure
probeAnnotation-class | Class "probeAnnotation"
samplePointMatrix-class | Sample point matrix
show,compKc-method | KC smart comparative
show,compKcSigRegions-method | KC smart comparative
show,samplePointMatrix-method | Sample point matrix
show,sigSegments-method | Significant segments
show,spmCollection-method | Sample point matrix collection
sigSegments-class | Significant segments
sort,KcghData,missing-method | Class "KcghData"
sort,KcghDataSum,missing-method | Class "KcghDataSum"
spmCollection-class | Sample point matrix collection
unlist,KCData-method | Internal class "KCData"
write.table | Write summary of the significant regions to a table
write.table,compKcSigRegions-method | Write summary of the significant regions to a table
write.table,sigSegments-method | Write summary of the significant regions to a table
[,probeAnnotation-method | Class "probeAnnotation"
[[,KCData-method | Internal class "KCData"
[[<-,KCData-method | Internal class "KCData"