dmrff.meta: dmrff.meta

In perishky/dmrff: Identifying differentially methylated regions efficiently with power and control

dmrff.meta

Description

Identify differentially methylated regions by meta-analysing multiple studies using variance-weighted fixed effects meta-analysis.

Usage

dmrff.meta(objects, maxgap = 500, p.cutoff = 0.05, verbose = T)

Arguments

objects	List of objects generated by dmrff.pre for each participating EWAS.
maxgap	Maximum distance between consecutive features (Default: 500bp).
p.cutoff	Unadjusted p-value cutoff for membership in a candidate DMR (Default: 0.05).
verbose	If TRUE (default), then output status messages.

Details

Warning! Ensure that the order of the CpG sites corresponding to the the rows of 'methylation' match the order of the CpG sites corresponding to the other variables, e.g. 'estimate' and 'chr'.

Value

A data frame listing all candidate regions and their summary statistics.

Examples

pre1 <- dmrff.pre(est1, se1, meth1, ...)
pre2 <- dmrff.pre(est2, se2, meth2, ...)
...
pre9 <- dmrff.pre(est9, se9, meth9, ...)
meta <- dmrff.meta(list(pre1, pre2, ..., pre9))
meta$dmrs[which(meta$dmrs$p.adjust < 0.05 & meta$dmrs$n > 1), ]

perishky/dmrff documentation built on Jan. 4, 2024, 10:23 p.m.