detectionPoobEcdf2 {sesame}R Documentation

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

Description

aka pOOBAH2 (p-vals by Out-Of-Band Array Hybridization)

Usage

detectionPoobEcdf2(
  sdf,
  return.pval = FALSE,
  combine.neg = TRUE,
  pval.threshold = 0.05
)

pOOBAH2(sdf, return.pval = FALSE, combine.neg = TRUE, pval.threshold = 0.05)

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

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.

The difference between this function and the original pOOBAH is that pOOBAH2 is based on background-subtracted and dyebias corrected signal and do not distinguish the color channel difference.

Value

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

Examples

sdf <- sesameDataGet("EPIC.1.SigDF")
sum(sdf$mask)
sdf <- detectionPoobEcdf2(sdf)
sum(sdf$mask)
sdf <- sesameDataGet("EPIC.1.SigDF")
sum(sdf$mask)
sdf <- pOOBAH2(sdf)
sum(sdf$mask)

[Package sesame version 1.12.0 Index]