Overview | From raw to segmented data | From raw data to segment list | Identifying Segment Gain Or Loss (SGOL) | Identifying Minimum Common Regions (MCR) | Session Information | References
Package: cghMCR 1.71.0
J. Zhang
cghMCR: Find chromosome regions showing common gains/losses
This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.
Authors:
cghMCR_1.71.0.tar.gz
cghMCR_1.71.0.zip(r-4.7)cghMCR_1.71.0.zip(r-4.6)cghMCR_1.71.0.zip(r-4.5)
cghMCR_1.71.0.tgz(r-4.6-any)cghMCR_1.71.0.tgz(r-4.5-any)
cghMCR_1.71.0.tar.gz(r-4.7-any)cghMCR_1.71.0.tar.gz(r-4.6-any)
cghMCR_1.71.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
cghMCR/json (API)
| # Install 'cghMCR' in R: |
| install.packages('cghMCR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- segData - The constructor for the cghMCR class
On BioConductor:cghMCR-1.71.0(bioc 3.24)cghMCR-1.70.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:aafc41391a. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 176 | ||
| linux-devel-x86_64 | WARNING | 254 | ||
| source / vignettes | OK | 256 | ||
| linux-release-x86_64 | WARNING | 249 | ||
| macos-release-arm64 | WARNING | 145 | ||
| macos-oldrel-arm64 | WARNING | 165 | ||
| windows-devel | WARNING | 179 | ||
| windows-release | WARNING | 169 | ||
| windows-oldrel | WARNING | 182 | ||
| wasm-release | OK | 153 |
Exports:cghMCRgolMCRmergeMCRProbesplotplot.DNAcopySGOL
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemcliCNToolscpp11crayoncurlDBIDNAcopyfastmapgenefiltergenericsgluehttrIRangesjsonliteKEGGRESTlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6rlangRSQLiteS4VectorsSeqinfostatmodsurvivalsysvctrsXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The constructor for the cghMCR class | cghMCR segData |
| Class "cghMCR" is a S4 class for the identification of minimum common regions of gains or losses across samples | cghMCR-class getSegments getSegments,marrayNorm-method getSegments,marrayRaw-method MCR MCR,cghMCR-method |
| Methods for Function colnames/rownames in Package `cghMCR' | colnames,SGOL-method colnames-methods rownames,SGOL-method rownames-methods [,SGOL-method [-methods |
| A function that appends probe ids to a data frame containing MCRs | mergeMCRProbes |
| A function to plot the original data along with the segments identified using segment of DNAcopy. | plot.DNAcopy |
| Class "SGOL" reprents segments of gain or loss across samples | gol gol,SGOL-method method,SGOL-method plot plot,ANY-method plot,methods plot,SGOL,ANY-method plot,SGOL-method SGOL SGOL-class threshold,SGOL-method |