Package: quantsmooth 1.73.0
Jan Oosting
quantsmooth: Quantile smoothing and genomic visualization of array data
Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.
Authors:
quantsmooth_1.73.0.tar.gz
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quantsmooth.pdf |quantsmooth.html✨
quantsmooth/json (API)
| # Install 'quantsmooth' in R: |
| install.packages('quantsmooth', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- affy.cn - Example data from several quantitative genomic methods
- affy.pos - Example data from several quantitative genomic methods
- bac.cn - Example data from several quantitative genomic methods
- bac.pos - Example data from several quantitative genomic methods
- chrom.bands - Dataset of human chromosomes and their banding patterns
- chrom.bands.hg18 - Dataset of human chromosomes and their banding patterns
- chrom.bands.hg19 - Dataset of human chromosomes and their banding patterns
- chrom.bands.hg38 - Dataset of human chromosomes and their banding patterns
- chrom.bands.mm10 - Dataset of human chromosomes and their banding patterns
- ill.cn - Example data from several quantitative genomic methods
- ill.pos - Example data from several quantitative genomic methods
On BioConductor:quantsmooth-1.73.0(bioc 3.21)quantsmooth-1.72.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationcopynumbervariation
Last updated 2 months agofrom:eff14ecc0f. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:characterCHRdrawSimpleChromgetChangedIdxgetChangedRegionsgetLambdaMingrid.chromosomelengthChromosomenumericCHRpaintCytobandsplotChromosomeplotSmoothedposition2CytobandprepareGenomePlotquantsmoothquantsmooth.cvquantsmooth.segscaleto
Dependencies:latticeMASSMatrixMatrixModelsquantregSparseMsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dataset of human chromosomes and their banding patterns | chrom.bands chrom.bands.hg18 chrom.bands.hg19 chrom.bands.hg38 chrom.bands.mm10 |
| Example data from several quantitative genomic methods | affy.cn affy.pos bac.cn bac.pos chr14 ill.cn ill.pos |
| Draw chromosome-like icons | drawSimpleChrom |
| getChangedRegions | getChangedRegions |
| getLambdaMin | getLambdaMin |
| Draw a chromosome using the grid package | grid.chromosome |
| Retrieve chromosomal length | lengthChromosome |
| Conversion of chromosome IDs between numeric and character | characterCHR numericCHR |
| Paint a chromosomal idiogram | paintCytobands |
| Wrapper for plotSmoothed | plotChromosome |
| plotSmoothed | plotSmoothed |
| Determine cytoband position based on location of probe | position2Cytoband |
| Set up a full genome plot | prepareGenomePlot |
| quantsmooth | quantsmooth |
| quantsmooth.cv | quantsmooth.cv |
| quantsmooth.seg | quantsmooth.seg |
| Scales data within a range to a new range | scaleto |
