Create a ProteinExpressionAssay object — ProteinExpressionAssay • OncoProfilingTools

Creates a `ProteinExpressionAssay`, a `SummarizedExperiment` subclass for protein-coding gene expression data.

Usage

RNAAssay(
  data,
  rowData = NULL,
  colData = NULL,
  metadata = list(),
  assay_name = "RNA",
  unit = "log2(TPM+1)",
  normalized = TRUE,
  feature_type = "protein_coding_gene",
  source = NA_character_,
  source_file = NA_character_
)

Arguments

data: A numeric matrix-like object with features as rows and samples/models as columns.
rowData: Optional feature-level metadata. Must have one row per feature.
colData: Optional sample/model-level metadata. Must have one row per sample/model.
metadata: Optional assay-level metadata list.
assay_name: Name of the primary assay. Defaults to `"protein_expression"`.
unit: Character string describing the expression unit, such as `"log2(TPM+1)"`.
normalized: Logical scalar indicating whether the expression data are normalized.
feature_type: Character string describing the feature type, such as `"protein_coding_gene"`.
source: Optional character string describing the data source.
source_file: Optional character string storing the source file path.

Value

A `ProteinExpressionAssay` object.