Description Usage Arguments Value Examples

A thin wrapper that implements the main data-adaptive multiple hypothesis testing strategy for data structures commonly found in computational biology experiments, using the popular SummarizedExperiment container class.

1 2 3 4 |

`data_in` |
An object of class |

`var_int` |
A |

`cntrl_set` |
A |

`n_top` |
(integer vector) - value for the number of candidate covariates to generate using the data-adaptive estimation algorithm. |

`n_fold` |
(integer vector) - number of cross-validation folds. |

`parameter_wrapper` |
(function) - user-defined function that takes input
(Y, A, W, absolute, negative) and outputs a (integer vector) containing
ranks of biomarkers (outcome variables). For detail, please refer to the
documentation for |

`learning_library` |
(character vector) - library of learning algorithms to be used in fitting the "Q" and "g" step of the standard TMLE procedure. |

`absolute` |
(logical) - whether or not to test for absolute effect size.
If |

`negative` |
(logical) - whether or not to test for negative effect size.
If |

`p_cutoff` |
The minimum p-value required to evaluate a given biological unit (e.g., gene) as statistically significant. |

`q_cutoff` |
The minimum p-value required to evaluate a given biological unit (e.g., gene) as statistically significant after applying a correction for multiple hypothesis testing. |

An object of class `adaptmle`

, sub-classed from the popular
container class `SummarizedExperiment`

, containing information about
the experiment being analyzed as well as results from applying the TMLE for
the data-adaptive target parameter as produced by `adpatest`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
library(SummarizedExperiment)
library(airway)
set.seed(5678)
data(airway)
genes_sub <- order(sample(seq_len(100)))
air_reduced <- airway[genes_sub, ]
simple_air <- cbind(air_reduced, air_reduced)
dex_var = as.numeric(as.matrix(colData(simple_air))[, 3] - 1)
airway_out <- bioadaptest(data_in = simple_air,
var_int = dex_var,
cntrl_set = NULL,
n_top = 5,
n_fold = 2,
parameter_wrapper = rank_DE)
``` |

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