OmicSignature R6 object

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.

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

Public methods

• OmicSignature$new()

• OmicSignature$print()

• OmicSignature$extractSignature()

• OmicSignature$clone()

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Method 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

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Method print()

Print an OmicSignature object

Usage

OmicSignature$print()

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Method extractSignature()

Usage

OmicSignature$extractSignature(conditions)

Arguments

conditions

conditions for new signatures

Returns

a dataframe of new signatures

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Method clone()

The objects of this class are cloneable with this method.

Usage

OmicSignature$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.