Package: CGHbase 1.73.0
Mark van de Wiel
CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.
Contains functions and classes that are needed by arrayCGH packages.
Authors:
CGHbase_1.73.0.tar.gz
CGHbase_1.73.0.zip(r-4.7)CGHbase_1.73.0.zip(r-4.6)CGHbase_1.73.0.zip(r-4.5)
CGHbase_1.73.0.tgz(r-4.6-any)CGHbase_1.73.0.tgz(r-4.5-any)
CGHbase_1.73.0.tar.gz(r-4.7-any)CGHbase_1.73.0.tar.gz(r-4.6-any)
CGHbase_1.73.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CGHbase/json (API)
| # Install 'CGHbase' in R: |
| install.packages('CGHbase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tgac-vumc/cghbase/issues
Datasets:
- Wilting - Cervical cancer arrayCGH data
- WiltingCalled - Cervical cancer arrayCGH data called with CGHcall
- WiltingNorm - Normalized log2 ratios from cervical cancer arrayCGH data.
- WiltingRaw - Raw log2 ratios from cervical cancer arrayCGH data.
- WiltingRegions - Regions of cervical cancer arrayCGH data as defined by CGHregions
- WiltingSeg - Segmented log2 ratios from cervical cancer arrayCGH data.
On BioConductor:CGHbase-1.73.0(bioc 3.24)CGHbase-1.72.0(bioc 3.23)
infrastructuremicroarraycopynumbervariation
Last updated from:961838b439. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 160 | ||
| linux-devel-x86_64 | NOTE | 185 | ||
| source / vignettes | OK | 155 | ||
| linux-release-x86_64 | NOTE | 133 | ||
| macos-release-arm64 | NOTE | 114 | ||
| macos-oldrel-arm64 | NOTE | 96 | ||
| windows-devel | NOTE | 90 | ||
| windows-release | NOTE | 84 | ||
| windows-oldrel | NOTE | 92 | ||
| wasm-release | OK | 91 |
Exports:avedistbpendbpstartcallscalls<-chromosomescopynumbercopynumber<-frequencyPlotfrequencyPlotCallsinitializemake_cghRawncloneplotplot.cghCallplot.cghRawplot.cghRegionsplot.cghSegprobampprobamp<-probdlossprobdloss<-probgainprobgain<-problossprobloss<-probnormprobnorm<-regionsregions<-segmentedsegmented<-summaryPlot
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CGHbase: Base functions and classes for arrayCGH data analysis. | CGHbase-package CGHbase |
| Retrieve regions information from cghRegions object. | avedist nclone |
| Class to contain and describe called array comparative genomic hybridization data. | bpend,cghCall-method bpstart,cghCall-method calls,cghCall-method calls<-,cghCall,matrix-method cghCall cghCall-class chromosomes,cghCall-method class:cghCall copynumber,cghCall-method copynumber<-,cghCall,matrix-method frequencyPlotCalls,cghCall,missing-method initialize,cghCall-method plot,cghCall,missing-method plot.summary,cghCall,missing-method probamp,cghCall-method probamp<-,cghCall,matrix-method probdloss,cghCall-method probdloss<-,cghCall,matrix-method probgain,cghCall-method probgain<-,cghCall,matrix-method probloss,cghCall-method probloss<-,cghCall,matrix-method probnorm,cghCall-method probnorm<-,cghCall,matrix-method segmented,cghCall-method segmented<-,cghCall,matrix-method |
| Class to contain and describe raw or normalized array comparative genomic hybridization data. | bpend,cghRaw-method bpstart,cghRaw-method cghRaw cghRaw-class chromosomes,cghRaw-method class:cghRaw copynumber,cghRaw-method copynumber<-,cghRaw,matrix-method initialize,cghRaw-method plot,cghRaw,missing-method |
| Class to contain and describe array comparative genomic hybridization regions data. | avedist,cghRegions-method bpend,cghRegions-method bpstart,cghRegions-method cghRegions cghRegions-class chromosomes,cghRegions-method class:cghRegions frequencyPlot,cghRegions,missing-method initialize,cghRegions-method nclone,cghRegions-method plot.cghRegions,cghRegions,missing-method regions,cghRegions-method regions<-,cghRegions,matrix-method |
| Class to contain and describe segmented array comparative genomic hybridization data. | bpend,cghSeg-method bpstart,cghSeg-method cghSeg cghSeg-class chromosomes,cghSeg-method class:cghSeg copynumber,cghSeg-method copynumber<-,cghSeg,matrix-method initialize,cghSeg-method plot,cghSeg,missing-method segmented,cghSeg-method segmented<-,cghSeg,matrix-method |
| Retrieve feature position data from cgh objects. | bpend bpstart chromosomes |
| Retrieve copynumber data from cgh objects. | calls calls<- copynumber copynumber<- segmented segmented<- |
| Visualization of aCGH regions. | frequencyPlot |
| Visualization of aCGH profiles. | frequencyPlotCalls |
| Convert a dataframe or textfile to an object of class cghRaw. | make_cghRaw |
| Plot aCGH data. | plot.cghCall plot.cghRaw plot.cghRegions plot.cghSeg |
| Retrieve call probabilities from a cghCall object. | probamp probamp<- probdloss probdloss<- probgain probgain<- probloss probloss<- probnorm probnorm<- |
| Retrieve regions data from cghRegions object. | regions regions<- |
| Visualization of aCGH profiles. | summaryPlot |
| Cervical cancer arrayCGH data | Wilting |
| Cervical cancer arrayCGH data called with CGHcall | WiltingCalled |
| Normalized log2 ratios from cervical cancer arrayCGH data. | WiltingNorm |
| Raw log2 ratios from cervical cancer arrayCGH data. | WiltingRaw |
| Regions of cervical cancer arrayCGH data as defined by CGHregions | WiltingRegions |
| Segmented log2 ratios from cervical cancer arrayCGH data. | WiltingSeg |
