Package: saasCNV 0.3.4
saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data
Perform joint segmentation on two signal dimensions derived from total read depth (intensity) and allele specific read depth (intensity) for whole genome sequencing (WGS), whole exome sequencing (WES) and SNP array data.
Authors:
saasCNV_0.3.4.tar.gz
saasCNV_0.3.4.zip(r-4.5)saasCNV_0.3.4.zip(r-4.4)saasCNV_0.3.4.zip(r-4.3)
saasCNV_0.3.4.tgz(r-4.4-any)saasCNV_0.3.4.tgz(r-4.3-any)
saasCNV_0.3.4.tar.gz(r-4.5-noble)saasCNV_0.3.4.tar.gz(r-4.4-noble)
saasCNV_0.3.4.tgz(r-4.4-emscripten)saasCNV_0.3.4.tgz(r-4.3-emscripten)
saasCNV.pdf |saasCNV.html✨
saasCNV/json (API)
| # Install 'saasCNV' in R: |
| install.packages('saasCNV', repos = c('https://zhangzhongyang16.r-universe.dev', 'https://cloud.r-project.org')) |
- seq.cnv - Internal Functions and Data
- seq.data - Internal Functions and Data
- seq.segs - Internal Functions and Data
- seq.segs.merge - Internal Functions and Data
- snp.cnv - Internal Functions and Data
- snp.cnv.anno - Internal Functions and Data
- snp.cnv.refine - Internal Functions and Data
- snp.cnv.refine.anno - Internal Functions and Data
- snp.segs - Internal Functions and Data
- snp.segs.merge - Internal Functions and Data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 years agofrom:2b74d19991. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 17 2024 |
| R-4.5-win | OK | Sep 17 2024 |
| R-4.5-linux | OK | Sep 17 2024 |
| R-4.4-win | OK | Sep 17 2024 |
| R-4.4-mac | OK | Sep 17 2024 |
| R-4.3-win | OK | Sep 17 2024 |
| R-4.3-mac | OK | Sep 17 2024 |
Exports:BAF2mBAFcheck.overlapcnv.callcnv.datacnv.data.chrcompute.baselinecompute.baseline.manualcompute.varcomputeBetacomputeMomentscomputeTiltDirectComputeZ.fromS.RComputeZ.fromS.R.partialcomputeZ.onechangecomputeZ.onechange.samplecomputeZ.squarewave.sampledchidelta.sddiagnosis.cluster.plotdiagnosis.QQ.plotdiagnosis.seg.plot.chrfcompute.max.Zfmscbsfscan.maxGC.adjustgenome.wide.plotgetCutoffMultisampleWeightedChisqimpute.missing.datajoint.segmentationmatrix.maxmerging.segmentsmerging.segments.chrModemscbs.classifyNGS.CNVpmarg.sumweightedchisqpvalueMultisampleWeightedChisqreannotate.CNV.resseg.summarySNP.CNVsnp.cnv.datasnp.refine.boundaryvcf2txtvu
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data | saasCNV-package saasCNV |
| CNV Calling from Sequencing Data | cnv.call |
| Construct Data Frame for CNV Inference with NGS Data | cnv.data |
| Visualize Genome-Wide SCNA Profile in 2D Cluster Plot | diagnosis.cluster.plot |
| Visualize Segmentation Results for Diagnosis | diagnosis.seg.plot.chr |
| GC Content Adjustment | GC.adjust |
| Visualize Genome-Wide SCNA Profile | genome.wide.plot |
| Internal Functions and Data | BAF2mBAF check.overlap cnv.data.chr compute.baseline compute.baseline.manual compute.var computeBeta computeMoments computeTiltDirect ComputeZ.fromS.R ComputeZ.fromS.R.partial computeZ.onechange computeZ.onechange.sample computeZ.squarewave.sample dchi delta.sd diagnosis.QQ.plot fcompute.max.Z fmscbs fscan.max getCutoffMultisampleWeightedChisq impute.missing.data matrix.max merging.segments.chr Mode mscbs.classify pmarg.sumweightedchisq pvalueMultisampleWeightedChisq seg.summary seq.cnv seq.data seq.segs seq.segs.merge snp.cnv snp.cnv.anno snp.cnv.refine snp.cnv.refine.anno snp.data snp.segs snp.segs.merge snp_table vcf_table vu |
| Joint Segmentation on log2ratio and log2mBAF Dimensions | joint.segmentation |
| Merge Adjacent Segments | merging.segments |
| CNV Analysis Pipeline for WGS and WES Data | NGS.CNV |
| Gene Annotation | reannotate.CNV.res |
| CNV Analysis Pipeline for SNP array Data | SNP.CNV |
| Construct Data Frame for CNV Inference with SNP Array Data | snp.cnv.data |
| Refine Segment Boundaries | snp.refine.boundary |
| Covert VCF File to A Data Frame | vcf2txt |
