OmicSignature R6 object — OmicSignature • OmicSignature

An R6 object to store signatures generated from experiments, including metadata, signature, and an optional differential expression analysis result dataframe.

`OmicSignature` uses R6 reference semantics: assigning an object to a new variable does not make an independent copy. Both variables point to the same mutable object, so changes through one variable are visible through the other. Use `$clone()` when an independent copy is needed, and `$clone(deep = TRUE)` when nested R6 objects also need to be copied. updated 10/2025

Active bindings

metadata: a list to describe the metadata
signature: a dataframe contains probe_id, feature_name, score (optional) and group_label (optional)
difexp: a dataframe for differential expression result
removeDifexp: a function to remove difexp from the object

Methods

`OmicSignature$new()`

Create a new OmicSignature object

Usage

OmicSignature$new(metadata, signature, difexp = NULL, print_message = FALSE)

Arguments

metadata: required. a list. See `createMetadata` for more information
signature: required. a vector, or a dataframe including columns: "probe_id", "feature_name" and "group_label", and an optional column "score"
difexp: optional
print_message: use TRUE if want to see all messages printed

`OmicSignature$print()`

Print an OmicSignature object

Usage

OmicSignature$print()

`OmicSignature$extractSignature()`

Usage

OmicSignature$extractSignature(conditions)

Arguments

conditions: A character string of R expressions passed to `dplyr::filter()`, e.g. `"score > 5; adj_p < 0.01"`. Evaluated as R code (via `rlang::parse_exprs()`) against `difexp`, so `conditions` must only ever come from a trusted source, not from untrusted/external input.

Returns

a dataframe of new signatures

`OmicSignature$clone()`

The objects of this class are cloneable with this method.

Usage

OmicSignature$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.