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:Julian Stamp [cre, aut], Lorin Crawford [aut], sriramlab [cph], Blue Brain Project/EPFL [cph]

smer_0.0.1.tar.gz
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://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lcrawlab/sme/issues

Pkgdown site:https://lcrawlab.github.io

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

genomewideassociationepistasisgeneticssnplinearmixedmodelzlibcppopenmp

3.48 score 8 scripts 6 exports 67 dependencies

Last updated 14 days agofrom:5cd9a31c3e. Checks:2 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 17 2025
R-4.5-linux-x86_64OKJan 17 2025

Exports:approximate_memory_requirementscreate_hdf5_fileread_hdf5_datasetsimulate_traitssmewrite_hdf5_dataset

Dependencies:backportsBHbitbit64briocallrcheckmateclicliprcodetoolsCompQuadFormcpp11crayondescdiffobjdigestdplyrevaluatefansiFMStableforeachfsgenericsgenioglueharmonicmeanphmsiteratorsjsonlitelifecycleloggingmagrittrmvMAPITmvtnormpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspspurrrR6RcppRcppArmadilloRcppEigenRcppParallelRcppProgressRcppSpdlogreadrRhdf5librlangrprojrootstringistringrtestthattibbletidyrtidyselecttzdbutf8vctrsvroomwaldowithr

Conditioning Epistasis Search on Open Chromatin

Rendered fromstudy-erythroid-differentiation-data.Rmdusingknitr::rmarkdownon Jan 17 2025.

Last update: 2025-01-16
Started: 2025-01-16

How To Cite Our Work

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How To Create a Mask File

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How To Optimize the Memory Requirements of SME

Rendered fromtutorial-memory-optimization.Rmdusingknitr::rmarkdownon Jan 17 2025.

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How To Simulate Traits

Rendered fromtutorial-simulate-traits.Rmdusingknitr::rmarkdownon Jan 17 2025.

Last update: 2025-01-16
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How To Use the Sparse Marginal Epistasis Test

Rendered fromsmer.Rmdusingknitr::rmarkdownon Jan 17 2025.

Last update: 2025-01-16
Started: 2025-01-16