Package: KCsmart 2.71.0

Jorma de Ronde

KCsmart: Multi sample aCGH analysis package using kernel convolution

Multi sample aCGH analysis package using kernel convolution

Authors:Jorma de Ronde, Christiaan Klijn, Arno Velds

KCsmart_2.71.0.tar.gz
KCsmart_2.71.0.zip(r-4.7)KCsmart_2.71.0.zip(r-4.6)KCsmart_2.71.0.zip(r-4.5)
KCsmart_2.71.0.tgz(r-4.6-any)KCsmart_2.71.0.tgz(r-4.5-any)
KCsmart_2.71.0.tar.gz(r-4.7-any)KCsmart_2.71.0.tar.gz(r-4.6-any)
KCsmart_2.71.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
KCsmart/json (API)

# Install 'KCsmart' in R:

install.packages('KCsmart', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

hsMirrorLocs - Mirror locations of the human genome
hsSampleData - Homo Sapiens artificial cgh data set
mmMirrorLocs - Mirror locations of the mouse genome

On BioConductor:KCsmart-2.71.0(bioc 3.24)KCsmart-2.70.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

copynumbervariation visualization acgh microarray

3.60 score 1 scripts 2 mentions 13 exports 11 dependencies

Last updated from:3ca1da3b7a. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	147
linux-devel-x86_64	WARNING	225
source / vignettes	OK	160
linux-release-x86_64	WARNING	173
macos-release-arm64	WARNING	96
macos-oldrel-arm64	WARNING	124
windows-devel	WARNING	112
windows-release	WARNING	110
windows-oldrel	WARNING	134
wasm-release	OK	86

Exports:calcSpm calcSpmCollection compareSpmCollection findSigLevelFdr findSigLevelTrad getSigRegionsCompKC getSigSegments idPoints initialize plot plotScaleSpace show write.table

Dependencies:Biobase BiocGenerics generics KernSmooth lattice MASS Matrix multtest scrime siggenes survival

KCsmart example session

Rendered fromKCS.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

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