seabi {wateRmelon} | R Documentation

## Calculate a performance metric based on male-female differences for Illumina methylation 450K arrays

### Description

Calculates an area under ROC curve - based metric for Illumina 450K data using a t-test for male-female difference as the predictor for X-chromosome location of probes. The metric is 1-area so that small values indicate good performance, to match our other, standard error based metrics `gcose` and `dmrse`. Note that this requires both male and female samples of known sex and can be slow to compute due to running a t-test on every probe.

### Usage

    seabi(bn, stop = 1, sex, X)

### Arguments

`bn` | a matrix of betas (default method) or an object containing betas i.e. a `MethyLumiSet` object (`methylumi` package), a `MethylSet` or `RGChannelSet` object (`minfi` package) or a `exprmethy450` object (`IMA` package).
`stop` | partial area under curve is calculated if stop value <1 is provided
`sex` | a factor giving the sex of each sample (column)
`X` | a logical vector of length equal to the number of probes, true for features mapped to X-chromosome

### Value

a value between 0 and 1. values close to zero indicate high data quality as judged by the ability to discriminate male from female X-chromosome DNA methylation.

### Author(s)

leonard.schalkwyk@kcl.ac.uk

### References

Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)

### Examples

       library(methylumi)
       data(melon)
       sex  <- pData(melon)$sex
       X    <- melon@featureData@data$CHR=='X'
       seabi(betas(melon), sex=sex, X=X)

    # methylumi method
       seabi(melon, sex=sex, X=X)

[Package wateRmelon version 1.28.0 Index]