CpGannotated-class: An object summarising individual CpG sites fitted to a given...

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

An object summarising individual CpG sites fitted to a given model

Description

An S4 class that stores output from either cpg.annotate or sequencing.annotate.

Slots

ranges:

A GRanges object, containing CpG-level information to be passed to dmrcate. Mcols of this object include:

- stat: Per-CpG test statistic; t if from limma or Wald if from DSS if using differential mode. Variance if using variability mode, sqrt(F) if using ANOVA mode, t if using diffVar mode.

- rawpval: Raw p-value from DMP fitting.

- diff: Methylation difference/coefficient. In beta space for cpg.annotate output and output passed from DSS::DMLtest(). In logit space for when a BSseq object is passed from sequencing.annotate. Not available for output passed from DSS::DMLtest.multiFactor(). Not applicable in variability, ANOVA or diffVar modes.

- ind.fdr: False discovery rate as calculated on individual CpG sites.

- is.sig: Logical determining whether a CpG site is individually significant or not. Can be adjusted using changeFDR.

betas:

A matrix of per-CpG beta values matching the annotated loci.

Methods

CpGannotated objects have a show method that describes the data therein.

Author(s)

Tim Peters <[e-mail]>

timpeters82/DMRcate-devel documentation built on Oct. 2, 2024, 10:33 a.m.