Skip to contents

Filter an mmo object by samples, groups, and/or features

filter_mmo.Rd

Subset all components of an mmo object (feature tables, metadata, distance matrices, and annotations) to a given set of samples, groups, and/or feature IDs. Filtering is applied consistently across all slots present in mmo.

Optionally, if an mgf_path is provided, a filtered MGF is written containing only spectra for the retained features (using filter_mgf_to_mmo()).

Usage

filter_mmo(
  mmo,
  sample_list = NULL,
  group_list = NULL,
  id_list = NULL,
  sample_col = "sample",
  group_col = "group",
  drop_empty_feat = TRUE,
  empty_threshold = NULL,
  mgf_path = NULL,
  output_path = NULL
)

Arguments

mmo

A list-like mmo object as returned by GetMZmineFeature().

sample_list

Optional character vector of sample IDs (matching sample_col in mmo$metadata) to retain.

group_list

Optional character vector of group labels (matching group_col in mmo$metadata) to retain. Mutually exclusive with sample_list.

id_list

Optional character vector of feature IDs to retain. If NULL, features are determined from feature_data and optionally filtered by drop_empty_feat.

sample_col

Column name in mmo$metadata containing sample IDs. Default is "sample".

group_col

Column name in mmo$metadata containing group labels. Default is "group".

drop_empty_feat

Logical; if TRUE (default) drop features with no non-zero values in the retained samples.

empty_threshold

Optional numeric threshold used to define “empty” features. If NULL (default), the smallest positive, non-NA intensity in the retained samples is used. Features are kept if they have at least one value > threshold across retained samples.

mgf_path

Optional character. If provided, an MGF file will be filtered to retained features using filter_mgf_to_mmo().

output_path

Character or NULL. Passed to filter_mgf_to_mmo(). If NULL (default), output is "<input>_filtered.mgf".

Value

A filtered mmo object with the same structure as mmo, but restricted to the requested samples / groups / features. If mgf_path is provided, the returned object also includes mmo_filtered$mgf_filtered_path.

Examples

if (FALSE) { # \dontrun{
mmo_sub <- filter_mmo(mmo, group_list = c("Species1", "Species2"))

# Also write a filtered mgf:
mmo_sub <- filter_mmo(mmo, group_list = c("Species1", "Species2"),
                      mgf_path = "spectra.mgf")
} # }