pOOBAH: Detection P-value based on ECDF of out-of-band signal

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

Detection P-value based on ECDF of out-of-band signal

Description

aka pOOBAH (p-vals by Out-Of-Band Array Hybridization)

Usage

pOOBAH(
  sdf,
  return.pval = FALSE,
  combine.neg = TRUE,
  pval.threshold = 0.05,
  verbose = FALSE
)

Arguments

sdf	a SigDF
return.pval	whether to return p-values, instead of a masked SigDF
combine.neg	whether to combine negative control probes with the out-of-band probes in simulating the signal background
pval.threshold	minimum p-value to mask
verbose	print more messages

Details

The function takes a SigDF as input, computes detection p-value using out-of-band probes empirical distribution and returns a new SigDF with an updated mask slot.

Value

a SigDF, or a p-value vector if return.pval is TRUE

Examples

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

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