In wilsoncai1992/adaptest: Data-Adaptive Statistics for High-Dimensional Multiple Testing

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R/adaptest

Data-adaptive statistics for multiple testing in high-dimensional biology

Authors: Wilson Cai and Nima Hejazi

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What's adaptest?

The adaptest R package is a tool for performing multiple testing on effect sizes in high-dimensional settings, using the approach of data-adaptive statistical target parameters and inference. For technical details on the data-adaptive multiple testing procedure, consult @cai2018data. For an introduction to statistical inference procedures using data-adaptive target parameters, the interested reader is directed to @hubbard2016statistical.

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Installation

For standard use, install from Bioconductor using BiocManager:

if (!requireNamespace("BiocManager", quietly=TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("adaptest")

To contribute, install the development version (i.e., branch master) from GitHub via devtools:

devtools::install_github("wilsoncai1992/adaptest")

Current and prior Bioconductor releases are available under branches with numbers prefixed by "RELEASE_". For example, to install the version of this package available via Bioconductor 3.7, use

devtools::install_github("wilsoncai1992/adaptest", ref = "RELEASE_3_7")

Note: As the first stable release of this package was through Bioconductor v3.7, the minimum version of R required to install adaptest is 3.5.0 (codename "Joy in Playing").

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Example

For details on how to best use the adaptest R package, please consult the most recent package vignette available through the Bioconductor project.

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Issues

If you encounter any bugs or have any specific feature requests, please file an issue.

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Contributions

Contributions are very welcome. Interested contributors should consult our contribution guidelines prior to submitting a pull request.

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Citation

After using the adaptest R package, please cite the following

  @article{cai2018adaptest,
    doi = {10.21105/joss.00161},
    url = {https://doi.org/10.21105/joss.00161},
    year  = {2018},
    month = {October},
    publisher = {The Open Journal},
    volume = {3},
    number = {30},
    author = {Cai, Weixin and Hubbard, Alan E and Hejazi, Nima S},
    title = {{adaptest}: Data-Adaptive Statistics for High-Dimensional
      Testing in {R}},
    journal = {The Journal of Open Source Software}
  }

  @article{cai2018+adaptive,
    url = {https://arxiv.org/abs/1704.07008},
    year  = {2018+},
    author = {Cai, Weixin and Hejazi, Nima S and Hubbard, Alan E},
    title = {Data-adaptive statistics for multiple hypothesis testing in
      high-dimensional settings}
  }

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Funding

The development of this software was supported in part through grants from the National Institutes of Health: P42 ES004705-29 and T32 LM012417-02.

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License

© 2017-2018 Wilson Cai

The software contents of this repository are distributed under the GPL-2 license. See file LICENSE for details.

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References

wilsoncai1992/adaptest documentation built on Jan. 6, 2020, 2:33 p.m.