Package: smer 0.0.1
Julian Stamp
smer: Sparse Marginal Epistasis Test
The Sparse Marginal Epistasis Test is a computationally efficient genetics method which detects statistical epistasis in complex traits; see Stamp et al. (2025, <doi:10.1101/2025.01.11.632557>) for details.
Authors:
smer_0.0.1.tar.gz
smer_0.0.1.zip(r-4.5)smer_0.0.1.zip(r-4.4)
smer_0.0.1.tar.gz(r-4.5-noble)smer_0.0.1.tar.gz(r-4.4-noble)
smer.pdf |smer.html✨
smer/json (API)
NEWS
| # Install 'smer' in R: |
| install.packages('smer', repos = c('https://lcrawlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lcrawlab/sme/issues
Pkgdown site:https://lcrawlab.github.io
- getting_started - Simulated Dataset for Genome-Wide Interaction Analysis
genomewideassociationepistasisgeneticssnplinearmixedmodelzlibcppopenmp
Last updated 15 days agofrom:b778e0ae78. Checks:3 OK, 1 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 17 2025 |
| R-4.5-win-x86_64 | OK | Jan 17 2025 |
| R-4.5-linux-x86_64 | OK | Jan 17 2025 |
| R-4.4-win-x86_64 | NOTE | Jan 17 2025 |
Exports:approximate_memory_requirementscreate_hdf5_fileread_hdf5_datasetsimulate_traitssmewrite_hdf5_dataset
Dependencies:backportsBHbitbit64briocallrcheckmateclicliprcodetoolsCompQuadFormcpp11crayondescdiffobjdigestdplyrevaluatefansiFMStableforeachfsgenericsgenioglueharmonicmeanphmsiteratorsjsonlitelifecycleloggingmagrittrmvMAPITmvtnormpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspspurrrR6RcppRcppArmadilloRcppEigenRcppParallelRcppProgressRcppSpdlogreadrRhdf5librlangrprojrootstringistringrtestthattibbletidyrtidyselecttruncnormtzdbutf8vctrsvroomwaldowithr
Conditioning Epistasis Search on Open Chromatin
Rendered fromstudy-erythroid-differentiation-data.Rmdusingknitr::rmarkdownon Jan 17 2025.Last update: 2025-01-17
Started: 2024-12-15
How To Cite Our Work
Rendered fromtutorial-cite-us.Rmdusingknitr::rmarkdownon Jan 17 2025.Last update: 2025-01-14
Started: 2024-12-15
How To Create a Mask File
Rendered fromtutorial-create-mask-file.Rmdusingknitr::rmarkdownon Jan 17 2025.Last update: 2025-01-14
Started: 2024-12-15
How To Optimize the Memory Requirements of SME
Rendered fromtutorial-memory-optimization.Rmdusingknitr::rmarkdownon Jan 17 2025.Last update: 2025-01-17
Started: 2024-12-15
How To Simulate Traits
Rendered fromtutorial-simulate-traits.Rmdusingknitr::rmarkdownon Jan 17 2025.Last update: 2025-01-14
Started: 2024-12-15
How To Use the Sparse Marginal Epistasis Test
Rendered fromsmer.Rmdusingknitr::rmarkdownon Jan 17 2025.Last update: 2025-01-17
Started: 2025-01-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimate Memory Requirements for SME Routine | approximate_memory_requirements |
| Create an HDF5 File | create_hdf5_file |
| Simulated Dataset for Genome-Wide Interaction Analysis | getting_started |
| Read Dataset from an HDF5 File | read_hdf5_dataset |
| Simulate Quantitative Traits from PLINK Genotypes | simulate_traits |
| Sparse Marginal Epistasis Test (SME) | sme |
| Write Data to an HDF5 Dataset | write_hdf5_dataset |
