Import analysis metadata

Imports analysis 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 analysis metadata must contain following columns: analysis_id and qc_type. Additional analysis metadata columns are described under details below.

Usage

import_metadata_analyses(
  data = NULL,
  table = NULL,
  path = NULL,
  sheet = NULL,
  ignore_warnings = FALSE,
  excl_unmatched_analyses = FALSE
)

Arguments

data

A MRMhubExperiment object

table

A data frame or tibble with analysis (sample) 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

excl_unmatched_analyses

Exclude analyses (samples) that have no matching 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.

Examples

mexp <- MRMhubExperiment()
file_path = system.file("extdata", "MHQuant_demo.csv", package = "mrmhub")
mexp <- import_data_masshunter(
  data = mexp,
  path = file_path,
  import_metadata = FALSE)
#> ✔ Imported 38 analyses with 31 features.
#> ℹ feature_area selected as default feature intensity. Modify with `set_intensity_var()`.

meta_path = system.file("extdata", "MHQuant_demo_metadata_analyses.csv", package = "mrmhub")

mexp <- import_metadata_analyses(
  data = mexp,
  path = meta_path,
  excl_unmatched_analyses = TRUE)
#> ✔ Analysis metadata associated with 38 analyses.

print(mexp)
#> 
#> ── MRMhubExperiment:  ──────────────────────────────────────────────────────────
#> NA | 38 analyses and 31 features | signal: feature_area
#> Last step: Annotated raw AREA values
#> Normalized ✖ Quantitated ✖ Drift/batch ✖ Filtered ✖
#> ℹ Use `mrmhub_status()` for the full processing and metadata report