detectionCall {lumi} | R Documentation

## Estimate the detectable probe ratio

### Description

Estimate the detectable probe ratio of each probe, sample or just return an AP matrix

### Usage

    detectionCall(x.lumi, Th = 0.01, type = c('probe', 'sample', 'matrix'))

### Arguments

`x.lumi` | a LumiBatch or MethyLumiM object
`Th` | the threshold. By default, when the detection p-value is less than 0.01, we suppose it is detectable. For the old version of BeadStudio output (version 2 or earlier), the threshold will automatically transferred as 1 - Th, because in the old format, value close to 1 is suppose to be detectable.
`type` | determine to calculate the detection count by probe or by sample

### Value

If the type is 'probe', then returns the presentCount of each probe. If the type is 'sample', then return the detectable probe ratio of each sample. If the type is 'matrix', then return the AP matrix, in which 'A' represents absent (the detect p-value less than threshold) and 'P' represents present.

### Author(s)

Pan Du

### See Also

`lumiQ`

### Examples

    ## load example data
    data(example.lumi)
    ## load example data
    data(example.lumi)

    ## estimate the detect call (percentage of expressed genes) of each sample
    temp <- detectionCall(example.lumi, type='sample')
    print(temp)

    ## estimate the present count of each gene (probe)
    temp <- detectionCall(example.lumi, type='probe')
    hist(temp)

[Package lumi version 2.44.0 Index]