wateRmelon (version 1.16.0)

dmrse: 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.

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)