Filter low-quality features in omics assays — filter

This function applies variance- or expression-based filtering across one or more assays within a MultiAssayExperiment object. It is useful for removing low-quality or uninformative features before downstream analysis.

Usage

filter_omics(
  expomicset,
  method = c("variance", "expression"),
  assays = NULL,
  assay_name = 1,
  min_var = 1e-05,
  min_value = 5,
  min_prop = 0.7,
  verbose = TRUE
)

Arguments

expomicset: A MultiAssayExperiment object containing omics assays.
method: Filtering method: either "variance" or "expression".
assays: Character vector of assay names to filter. If NULL, all assays are filtered.
assay_name: Name or index of the assay within each SummarizedExperiment to use.
min_var: Minimum variance threshold (used if method = "variance").
min_value: Minimum expression value (used if method = "expression").
min_prop: Minimum proportion of samples exceeding min_value (used if method = "expression").
verbose: Whether to print messages for each assay being filtered.

Value

A filtered MultiAssayExperiment object with updated assays and step record.

Examples

if (FALSE) { # \dontrun{
filtered_expom <- filter_omics(
  method = c("variance"),
  assays = "Metabolomics",
  assay_name = 1,
  min_var = 0.01,
  verbose = TRUE)
} # }