Package: TriadSim 0.3.0
Min Shi
TriadSim: Simulating Triad Genomewide Genotypes
Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.
Authors:
TriadSim_0.3.0.tar.gz
TriadSim_0.3.0.tar.gz(r-4.5-noble)TriadSim_0.3.0.tar.gz(r-4.4-noble)
TriadSim_0.3.0.tgz(r-4.4-emscripten)TriadSim_0.3.0.tgz(r-4.3-emscripten)
TriadSim.pdf |TriadSim.html✨
TriadSim/json (API)
# Install 'TriadSim' in R: |
install.packages('TriadSim', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:8da5665b54. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 08 2024 |
R-4.5-linux | OK | Dec 08 2024 |
Exports:fit.risk.model.parget.brksget.target.genoglue.chr.segment.parpick_target.snpTriadSim
Dependencies:BiocGenericscodetoolsdoParallelforeachgenericsiteratorslatticeMatrixsnpStatssurvivalzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Resample families based on the risk model | fit.risk.model.par |
Picking chromosomal breaking points | get.brks |
Getting genotypes of the target SNPs | get.target.geno |
Splicing chromosomal segments | glue.chr.segment.par |
Pick target SNPs in the pathway | pick_target.snp |
An example recombination rate dataset | rcmb.rate |
SNPs in the PLINK files | snp.all2 |
Simulation main function | TriadSim |