empirical_pval: Calculate empirical region-level p-value

In DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

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.

DAMEfinder documentation built on Nov. 8, 2020, 11:10 p.m.