Import feature metadata

Imports feature metadata (annotation) from a preloaded data frame or tibble via the data argument, or from data from a file (CSV or Excel) via the path argument. The feature metadata must contain following column: feature_id. Additional feature metadata columns are described under details below.

Usage

import_metadata_features(
  data = NULL,
  table = NULL,
  path = NULL,
  sheet = NULL,
  ignore_warnings = FALSE
)

Arguments

data

A MRMhubExperiment object

table

A data frame or tibble with feature metadata. If path is also provided, an error will be raised.

path

A character string specifying the path to a CSV (.csv) or Excel (.xlsx) file. If table is also provided, an error will be raised.

sheet

Defines the sheet name in case an Excel file is provided.

ignore_warnings

Ignore warnings from data validation and proceed with importing metadata

Value

An updated MRMhubExperiment object

Identifier normalization

All imported identifiers are whitespace-normalized on import: leading and trailing spaces are removed and internal runs of whitespace are collapsed to a single space (for example "QC 01" becomes "QC 01"). Raw-data file extensions (.mzML, .d, .raw, .wiff, .wiff2, .lcd, .chrom, case-insensitive) are stripped from analysis_id.

The same normalization is applied to both the data and the metadata, which is what lets an analysis_id typed into metadata match the one derived from a data-file name instead of silently failing to join. A consequence is that two identifiers differing only by whitespace collapse to one and are then reported as duplicates.