dmrse {wateRmelon} | R Documentation

## Standard error of iDMR 450k array DNA methylation features

### Description

Imprinting differentially methylated regions (iDMRs) are expected to be approximately half methylated, as is observed at the 227 probes in known iDMRs. These functions calculate measures of dispersion for the beta values at these CpG sites, of which the most useful is dmrse_row, which is the between-sample standard error.

### Usage

    dmrse(betas, idmr = iDMR())
    dmrse_col(betas, idmr = iDMR())
    dmrse_row(betas, idmr = iDMR())

### Arguments

`betas` | a matrix of betas (default method), a `MethyLumiSet` object (`methylumi` package), a `MethylSet` or `RGChannelSet` object ( `minfi` package) or a `exprmethy450` object (`IMA` package).
`idmr` | a character vector of iDMR probe names such as returned by iDMR()

### Value

return a standard error of the mean of betas for all samples and iDMR probes (dmrse) or the standard error of the mean for just the between sample component(dmrse_row) or between probe(dmrse_col) component.

### 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)

### See Also

`seabi`, a sex-difference metric, and `genki`, based on SNPs.

### Examples

      #MethyLumiSet method
         data(melon)
         dmrse(melon)

      #MethyLumiSet method after normalization
         melon.dasen <- dasen(melon)
         dmrse(melon.dasen)

[Package wateRmelon version 1.22.1 Index]