wateRmelon: Illumina DNA methylation array normalization and metrics

metrics

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)

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.