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OmicModalitySpec R6 Class

Source: R/multi-omics.R
OmicModalitySpec.Rd

Specification for a single omics modality including data, preprocessing, and learner. Encapsulates everything needed to train/predict on one data type.

Public fields

id

Unique identifier for this modality (e.g., "mRNA", "miRNA")

x

Data matrix (samples x features)

learner

mlr3 Learner object

preproc

Optional mlr3pipelines Graph or PipeOp for preprocessing

Methods

Public methods

Method new()

Create a new modality specification

Usage

OmicModalitySpec$new(id, x, learner, preproc = NULL)

Arguments

id

Character, unique modality identifier

x

Matrix or data.frame with samples in rows, features in columns. Rownames should be sample IDs.

learner

mlr3 Learner or character shortcut (e.g., "classif.ranger")

preproc

Optional preprocessing pipeline (Graph or PipeOp)

Returns

An OmicModalitySpec object

Method get_sample_ids()

Get sample IDs for this modality

Usage

OmicModalitySpec$get_sample_ids()

Returns

Character vector of sample IDs

Method n_features()

Get number of features

Usage

OmicModalitySpec$n_features()

Returns

Integer

Method make_graph_learner()

Create a GraphLearner combining preprocessing and learner

Usage

OmicModalitySpec$make_graph_learner()

Returns

GraphLearner or Learner

Method as_task()

Create an mlr3 Task from this modality's data

Usage

OmicModalitySpec$as_task(
  y,
  target_name = "target",
  task_type = c("classif", "regr"),
  sample_ids = NULL
)

Arguments

y

Target vector (must align with rownames of x)

target_name

Name for target column

task_type

"classif" or "regr"

sample_ids

Optional subset of sample IDs to use

Returns

TaskClassif or TaskRegr

Method print()

Print method

Usage

OmicModalitySpec$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

OmicModalitySpec$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.