metrics: Calculate a full set of 450K normalization/performance...

In schalkwyk/wateRmelon: Illumina 450 and EPIC methylation array normalization and metrics

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)

[e-mail]

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 April 15, 2024, 12:06 p.m.