Skip to contents

Fix object for functioning of notame

Source: R/class_constructor.R
fix_object.Rd

Attempts to create missing columns in pheno and feature data. Optionally cleans the object and splits the object by mode. Modifies supplied "Sample_ID" column if needed. Aims to make the object compatible with all of notame.

Usage

fix_object(
  object,
  id_prefix = "ID_",
  id_column = NULL,
  split_by = NULL,
  name = NULL,
  clean = TRUE,
  split_data = FALSE,
  assay.type = NULL
)

Arguments

object

a SummarizedExperiment or MetaboSet object

id_prefix

character, prefix for autogenerated sample IDs, see Details

id_column

character, column name for unique identification of samples

split_by

character vector, in the case where all the modes are in the same object, the column names of feature data used to separate the modes (usually Mode and Column)

name

in the case where object only contains one mode, the name of the mode, such as "Hilic_neg"

clean

boolean, whether to select best classes, reorder columns and consistently rename columns in pheno and feature

split_data

logical, whether to split data by analytical mode recorded in the "Split" column of feature data. If TRUE (the default), will return a list of MetaboSet objects, one per analytical mode. If FALSE, will return a single MetaboSet object.

assay.type

character, assay to be used in case of multiple assays

Value

A new SummarizedExperiment object or MetaboSet object with a single peak table. If split_data = TRUE, a list containing separate objects for analytical modes.

Details

Only specify one of split_by and name. The feature data will contain columns named "Split", used to separate features from different modes, and "Flag" for recording flagged features. Unless a column named "Feature_ID" is found in feature data, a feature ID will be generated based on the value of "Split", mass and retention time. The function will try to find columns for mass and retention time by looking at a few common alternatives, and throw an error if no matching column is found. Sample information needs to contain a row called "Injection_order", and the values need to be unique. In addition, a possible sample identifier row needs to be named "Sample_ID", or to be specified in id_column, and the values need to be unique, with an exception of QC samples: if there are any "QC" identifiers, they will be replaced with "QC_1", "QC_2" and so on. If a "Sample_ID" column is not found, it will be created using the id_prefix and injection order or by renaming id_column.

Examples

data(example_set)
ex_set <- example_set
rowData(ex_set)$Flag <- NULL
fixed <- fix_object(ex_set)
#> INFO [2025-06-23 22:36:33] Pheno data was cleaned
#> INFO [2025-06-23 22:36:33] Initializing 'Flag' column with unflagged features
#> INFO [2025-06-23 22:36:33] Feature data was cleaned