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 1.12.9 Index]