Retrieve an expression matrix from a VISTA object — get_expression

Returns the specified assay (default "norm_counts") with optional gene/sample subsetting, replicate summarization by group, and simple transformations.

Usage

get_expression_matrix(
  x,
  assay_name = "norm_counts",
  genes = NULL,
  samples = NULL,
  group_column = NULL,
  summarise = FALSE,
  transform = c("none", "log2", "zscore")
)

Arguments

x: A VISTA object.
assay_name: Assay to extract (default: "norm_counts").
genes: Optional character vector of gene IDs to keep.
samples: Optional character vector of sample IDs (or group labels when summarise = TRUE) to keep.
group_column: Optional column in sample_info used when summarising replicates. Defaults to the stored group_column.
summarise: Logical; if TRUE, averages replicates per group_column.
transform: One of "none", "log2", or "zscore" applied after subsetting and optional summarisation. Z-scores are computed within the selected samples/columns.

Value

A numeric matrix with genes in rows and samples (or groups) in columns.