empirical_pval {DAMEfinder} | R Documentation

## Calculate empirical region-level p-value

### Description

This function permutes the coefficient of interest and re-runs `get_tstats` and `regionFinder` for each permutation. Code for permutations copied from the `dmrseq` function from the package of the same name.

### Usage

    empirical_pval(
      presa,
      design,
      rforiginal,
      coeff,
      cont,
      smooth,
      maxPerms = 10,
      Q,
      maxGap,
      method,
      ...
    )

### Arguments

`presa` | SExperiment output from `calc_derivedasm` or `calc_asm`.
`design` | design matrix.
`rforiginal` | data.frame of DAMEs calculated with original design.
`coeff` | Coefficient of interest to permute.
`cont` | same as in `get_tstats`.
`smooth` | Boolean.
`maxPerms` | Maximum possible permutations generated. Default = 10.
`Q` | Quantile for cuttof.
`maxGap` | Same as other functions in the package.
`method` | lmFit method.
`...` | Passed to `get_tstats` and then to `loessByCluster`.

### Value

Vector of empirical p-values.

[Package DAMEfinder version 1.6.0 Index]