Package: KCsmart 2.70.0
Jorma de Ronde
KCsmart: Multi sample aCGH analysis package using kernel convolution
Multi sample aCGH analysis package using kernel convolution
Authors:
KCsmart_2.70.0.tar.gz
KCsmart_2.70.0.zip(r-4.7)KCsmart_2.70.0.zip(r-4.6)KCsmart_2.70.0.zip(r-4.5)
KCsmart_2.70.0.tgz(r-4.6-any)KCsmart_2.70.0.tgz(r-4.5-any)
KCsmart_2.70.0.tar.gz(r-4.7-any)KCsmart_2.70.0.tar.gz(r-4.6-any)
KCsmart_2.70.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
KCsmart/json (API)
| # Install 'KCsmart' in R: |
| install.packages('KCsmart', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
- 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.
copynumbervariationvisualizationacghmicroarray
Last updated from:1bc5fe65e5 (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 148 | ||
| linux-devel-x86_64 | WARNING | 165 | ||
| source / vignettes | OK | 174 | ||
| linux-release-x86_64 | WARNING | 146 | ||
| macos-release-arm64 | WARNING | 152 | ||
| macos-oldrel-arm64 | WARNING | 156 | ||
| windows-devel | WARNING | 119 | ||
| windows-release | WARNING | 114 | ||
| windows-oldrel | WARNING | 125 | ||
| wasm-release | OK | 91 |
Exports:calcSpmcalcSpmCollectioncompareSpmCollectionfindSigLevelFdrfindSigLevelTradgetSigRegionsCompKCgetSigSegmentsidPointsinitializeplotplotScaleSpaceshowwrite.table
Dependencies:BiobaseBiocGenericsgenericsKernSmoothlatticeMASSMatrixmulttestscrimesiggenessurvival
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 |