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]