DMResults-class: Initial storage object for called DMRs - class

In timpeters82/DMRcate-devel: Methylation array and sequencing spatial analysis methods

Initial storage object for called DMRs - class

Description

An S4 class that stores DMR information as output from dmrcate.

Slots

This class has eight slots, summarising DMR information to be passed to extractRanges:

coord:

DMR coordinates in UCSC style.

no.cpgs:

Number of constituent CpG sites of DMR.

min_smoothed_fdr:

Minimum FDR of the smoothed estimate.

Stouffer:

Stouffer summary transform of the individual CpG p-values (FDR-corrected).

HMFDR:

Harmonic mean of the individual CpG p-values (FDR-corrected).

Fisher:

Fisher combined probability transform of the individual CpG p-values (FDR corrected).

maxdiff:

Maximum differential/coefficient within the DMR (logit2-space for sequencing mode).

meandiff:

Mean differential/coefficient across the DMR (logit2-space for sequencing mode).

Methods

DMResults objects have a show method describing the number of DMRs called.

Author(s)

Tim Peters <[e-mail]>

timpeters82/DMRcate-devel documentation built on Dec. 19, 2024, 11:14 a.m.