detectionPoobEcdf {sesame} | R Documentation

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

### Description

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

### Usage

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

    pOOBAH(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.

### Value

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

### Examples

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

    sdf <- sesameDataGet("EPIC.1.SigDF")
    sum(sdf$mask)
    sum(resetMask(sdf)$mask)
    sum(pOOBAH(sdf, pval.threshold=0.2)$mask)

[Package sesame version 1.12.9 Index]