CpGannotated-class: An object summarising individual CpG sites fitted to a given...
In timpeters82/DMRcate-devel: Methylation array and sequencing spatial analysis methods
CpGannotated-class R Documentation
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.
- 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.
Methods
CpGannotate objects have a show method that describes the data therein.
Author(s)
Tim Peters <t.peters@garvan.org.au>
timpeters82/DMRcate-devel documentation built on April 26, 2024, 9:23 a.m.
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| CpGannotated-class | R Documentation |
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
limmaor Wald if fromDSSif using differential mode. Variance if using variability mode, sqrt(F) if using ANOVA mode, t if using diffVar mode.- diff: Methylation difference/coefficient. In beta space for
cpg.annotateoutput and output passed fromDSS::DMLtest(). In logit space for when aBSseqobject is passed fromsequencing.annotate. Not available for output passed fromDSS::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.
Methods
CpGannotate objects have a show method that describes the data therein.
Author(s)
Tim Peters <t.peters@garvan.org.au>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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