Description Usage Arguments Details Value

This function runs the knockoff procedure from start to finish, creating the knockoffs, computing the test statistics, and selecting variables. It is the main entry point for the knockoff package.

1 2 3 |

`X` |
matrix or data frame of predictors |

`y` |
response vector |

`fdr` |
target FDR (false discovery rate) |

`statistic` |
the test statistic (by default, a lasso statistic). See the Details section for more information. |

`threshold` |
either 'knockoff' or 'knockoff+'. |

`knockoffs` |
either equicorrelated knockoffs ('equicorrelated') or knockoffs optimized using semidefinite programming ('sdp') |

`normalize` |
whether to scale the data columns to have unit norm. Only disable this if your data is already normalized. |

`randomize` |
whether randomization is to be used when constructing knockoffs and (when p < n < 2p) augmenting the model with extra rows |

The default test statistic is `knockoff.stat.lasso_signed_max`

.
Other useful test statistics include `knockoff.stat.fs`

and
`knockoff.stat.fs_omp`

. It is also possible to provide your own test
statistic (for an example, see the vignette).

To use SDP knockoffs, you must have a Python installation with CVXPY. For more information, see the vignette on SDP knockoffs:

`vignette('sdp', package='knockoff')`

An object of class "knockoff.result". This object is a list containing at least the following components:

`knockoff` |
matrix of knockoff variables |

`statistic` |
computed test statistic |

`threshold` |
computed selection threshold |

`selected` |
named vector of selected variables |

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