Structure of OmicSignature & OmicSignatureCollection
Vanessa Mengze Li
2026-07-22
Source:vignettes/ObjectStructure.Rmd
ObjectStructure.Rmd
OmicSignature object structure
An OmicSignature is an R6 object. Unlike most base R
objects, R6 objects use reference semantics: assigning an
OmicSignature to another variable does not create an
independent copy. Both variables point to the same mutable object, so
changes made through one variable are visible through the other. Use
OmS_copy <- OmS$clone() when you need an independent
object, and use OmS$clone(deep = TRUE) when nested R6
objects also need to be copied.
An OmicSignature object contains three parts:
- metadata, a list containing metadata fields;
- signature, a dataframe with the names, and directions
and scores if applicable, of the “significant” features;
- difexp, optional, a dataframe with the complete
differential expression analysis result.
See here for how to create one.
OmicSignatureCollection object structure
An OmicSignatureCollection is also an R6 object and
follows the same assignment-by-reference behavior. Use
$clone() before modifying a collection when you want to
keep the original object unchanged.
An OmicSignatureCollection object contains two
parts:
- metadata, a list containing a collection’s metadata fields; -
OmicSigList, a list of OmicSignature Objects
See here for how to create one.
