OmicSignatureCollection R6 object

An R6 object to store a collection of OmicSignature objects, including metadata and `OmicSigList`, a list of OmicSignature objects.

`OmicSignatureCollection` uses R6 reference semantics: assigning a collection 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

OmicSigList

a list of OmicSignature object(s)

Methods

Public methods

• OmicSignatureCollection$new()

• OmicSignatureCollection$print()

• OmicSignatureCollection$extractSignature()

• OmicSignatureCollection$metadataSummary()

• OmicSignatureCollection$clone()

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Method new()

Create an OmicSignatureCollection object

Usage

OmicSignatureCollection$new(metadata, OmicSigList, print_message = FALSE)

Arguments

metadata

required, must be a list

OmicSigList

required, a list of OmicSignature R6 objects

print_message

use TRUE if want to see all messages printed

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Method print()

Print an OmicSignatureCollection object

Usage

OmicSignatureCollection$print()

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Method extractSignature()

Usage

OmicSignatureCollection$extractSignature(conditions, bind = TRUE)

Arguments

conditions

conditions for new signatures

bind

use TRUE to return all results in a single dataframe. Otherwise, will return a list contains the result of each OmicSignature individually

Returns

a dataframe or a list of new signatures

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Method metadataSummary()

Usage

OmicSignatureCollection$metadataSummary(only_shared = TRUE)

Arguments

only_shared

use TRUE to only print the shared metadata fields in the OmicSignatures

Returns

a dataframe of the summary of the metadata

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Method clone()

The objects of this class are cloneable with this method.

Usage

OmicSignatureCollection$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.