Description Usage Arguments Value Examples

View source: R/prot_p_adjust.R

Given data frame or a vector of p-values, creates a data frame with column(s) containing p-values adjusted using one or more methods.

1 | ```
get_qvals(pvals, signs, method, threshold_excess1)
``` |

`pvals` |
A numeric vector of p-values (possibly with NAs). |

`signs` |
A numeric vector containing only -1, 1, 0 and NA. It indicates the sign of the corresponding T statistics. |

`method` |
Correction method. Can be abbreviated. Defaults to |

`threshold_excess1` |
A numeric value between 0 and 1 indicating the threshold at which correcting for an excess in p-values close to 1 should be performed. This is sometimes needed when a null distribution needs to be fitted. Note that the method still accounts for the total number of p-values when performing this correction. Only if there is, according to a binomial test, a significant enrichment of p-values above an automatically determined cut-off at the |

A data frame containing either one column with corrected p-values, or when `method = "fdrtool"`

, a data frame with three columns: p-values adjusted for scale and proportion of null values, q-values (FDR) and local fdr.

1 | ```
.....
``` |

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