keep_abundant

keep_abundant

# S4 method for class 'SummarizedExperiment'
keep_abundant(
  .data,
  abundance = assayNames(.data)[1],
  design = NULL,
  formula_design = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7,
  minimum_count_per_million = NULL,
  factor_of_interest = NULL,
  ...,
  .abundance = NULL
)

Arguments

.data

A `tbl` or `SummarizedExperiment` object containing transcript/gene abundance data

abundance, .abundance

The name of the transcript/gene abundance column (character, preferred)

design

A design matrix for more complex experimental designs. If provided, this is passed to filterByExpr instead of factor_of_interest.

formula_design

A formula for creating the design matrix

minimum_counts

The minimum count threshold for a feature to be considered abundant

minimum_proportion

The minimum proportion of samples in which a feature must be abundant

minimum_count_per_million

The minimum count per million threshold

factor_of_interest

The name of the column containing groups/conditions for filtering. DEPRECATED: Use 'design' or 'formula_design' instead.

...

Further arguments.

Value

A `SummarizedExperiment` object