detectionCall: Estimate the detectable probe ratio

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.