Package: BPM 1.0.0
Jianzhao Gao and Xiaodan Fan
BPM: Bayesian Purity Model to Estimate Tumor Purity
Bayesian purity model to estimate tumor purity using methylation array data (DNA methylation Infinium 450K array data) without reference samples.
Authors:
BPM_1.0.0.tar.gz
BPM_1.0.0.tar.gz(r-4.5-noble)BPM_1.0.0.tar.gz(r-4.4-noble)
BPM_1.0.0.tgz(r-4.4-emscripten)BPM_1.0.0.tgz(r-4.3-emscripten)
BPM.pdf |BPM.html✨
BPM/json (API)
| # Install 'BPM' in R: |
| install.packages('BPM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- annotGeneNames - Gene names of probes in 450K array dat
- goodProbes - Good probes in packages
- simUCEC - Simulated data to illustrate datasets in packages
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 years agofrom:2c0f4e4873. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 25 2024 |
| R-4.5-linux | OK | Aug 25 2024 |
Exports:ApiGetDMCsBayPMfullSampler
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| gene names of probes in 450K array dat | annotGeneNames |
| Get TOPK=500 DMCs and non-DMCs using moderated-t test | ApiGetDMCs |
| Bayesian Purity Model (BPM) Main functions. | BayPM |
| BPM software package | BPM-package BPM |
| Estimate noise intensity (nv) for non-DMCs, using maximum likelihood estmiation. | estimateNu |
| Sampling xi and alpha (tumor purity) | fullSampler |
| good probes in packages | goodProbes |
| Simulated data to illustrate datasets in packages | simUCEC |
