filterMetabolites {MetAlyzer}

Filter metabolites

Description

This function filters out certain classes or metabolites of the metabolites vector. If aggregated_data is not empty, metabolites and class will also be filtered here.

Usage

filterMetabolites(
  metalyzer_se,
  drop_metabolites = c("Metabolism Indicators"),
  drop_NA_concentration = FALSE,
  drop_quant_status = NULL,
  min_percent_valid = NULL,
  valid_status = c("Valid", "LOQ"),
  per_group = NULL,
  inplace = FALSE
)

Arguments

metalyzer_se

SummarizedExperiment

drop_metabolites

A character vector defining metabolite classes or individual metabolites to be removed

drop_NA_concentration

A boolean whether to drop metabolites which have any NAs in their concentration value

drop_quant_status

A character, vector of characters or list of characters specifying which quantification status to remove. Metabolites with at least one quantification status of this vector will be removed.

min_percent_valid

A numeric lower threshold between 0 and 1 (t less than or equal to x) to remove invalid metabolites that do not meet a given percentage of valid measurements per group (default per Metabolite).

valid_status

A character vector that defines which quantification status is considered valid.

per_group

A character vector of column names from meta_data that will be used to split each metabolite into groups. The threshold 'min_percent_valid' will be applied for each group. The selected columns from meta_data will be added to aggregated_data.

inplace

If FALSE, return a copy. Otherwise, do operation inplace and return None.

Value

An updated SummarizedExperiment

Examples

metalyzer_se <- MetAlyzer_dataset(file_path = example_extraction_data())

drop_metabolites <- c("C0", "C2", "C3", "Metabolism Indicators",
  inplace = TRUE
)
metalyzer_se <- filterMetabolites(metalyzer_se, drop_metabolites)
# or
filterMetabolites(metalyzer_se, drop_metabolites, inplace = TRUE)