# Multi sample aCGH analysis package using kernel convolution

## Documentation for package ‘KCsmart’ version 2.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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-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"