ELBAR: ELiminate BAckground-dominated Reading (ELBAR)

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

ELiminate BAckground-dominated Reading (ELBAR)

Description

ELiminate BAckground-dominated Reading (ELBAR)

Usage

ELBAR(
  sdf,
  return.pval = FALSE,
  pval.threshold = 0.05,
  margin = 0.05,
  capMU = 3000,
  delta.beta = 0.2,
  n.windows = 500
)

Arguments

sdf	a SigDF
return.pval	whether to return p-values, instead of a SigDF
pval.threshold	minimum p-value to mask
margin	the percentile margin to define envelope, the smaller the value the more aggressive the masking.
capMU	the maximum M+U to search for intermediate betas
delta.beta	maximum beta value change from sheer background-dominated readings
n.windows	number of windows for smoothing

Value

a SigDF with mask added

Examples

sdf <- sesameDataGet("EPIC.1.SigDF")
sum(sdf$mask)
sum(ELBAR(sdf)$mask)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.