metrics {wateRmelon} | R Documentation

## Calculate a full set of 450K normalization/performance metrics

### Description

Calculate X-chromosome, SNP and imprinting DMR metrics for a matrix of betas from an Illumina 450K Human DNA methylation array. Requires precalculated t-test p-values for sex differences, a list of X-chromosome features and of imprinting DMR features.

### Usage

    metrics(betas, pv, X, idmr = iDMR, subset = NULL)

### Arguments

`betas` | a matrix of betas, each row representing a probe, each column a sample
`pv` | a vector of p-values such as produced by `sextest`, one per row of betas
`X` | a logical vector of the same length as `pv`, indicating whether each probe is mapped to the X-chromosome
`idmr` | a character vector of probe names known to be in imprinting DMRs. Can be obtained with `iDMR()` or `data(iDMR)`
`subset` | index or character vector giving a subset of betas to be tested

### Value

`dmrse_row` | see `dmrse_row`
`dmrse_col` | see `dmrse_col`
`dmrse` | see `dmrse`
`gcoms_a` | see `genki`
`gcose_a` | see `genki`
`gcoms_b` | see `genki`
`gcose_b` | see `genki`
`gcoms_c` | see `genki`
`gcose_c` | see `genki`
`seabird` | see `seabi`

### 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

    data(melon)
    melon.dasen <- dasen(melon)
    bn <-betas(melon.dasen)
    X <- melon.dasen@featureData@data$CHR=='X'
    data(iDMR)
    sex <- pData(melon.dasen)$sex
    pv <- sextest(bn,sex)
    melon.metrics <- metrics(bn, pv, X, idmr = iDMR, subset = NULL)

[Package wateRmelon version 1.24.0 Index]