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 MidarExperiment 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 MidarExperiment object

Examples

mexp <- MidarExperiment()
file_path = system.file("extdata", "MHQuant_demo.csv", package = "midar")
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 = "midar")

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

print(mexp)
#> 
#> ── MidarExperiment ─────────────────────────────────────────────────────────────
#> Title:
#> 
#> Processing status: Annotated raw AREA values
#> 
#> ── Annotated Raw Data ──
#> 
#> • Analyses: 38
#> • Features: 31
#> • Raw signal used for processing: `feature_area`
#> 
#> ── Metadata ──
#> 
#> • Analyses/samples: ✔
#> • Features/analytes: ✖
#> • Internal standards: ✖
#> • Response curves: ✖
#> • Calibrants/QC concentrations: ✖
#> • Study samples: ✖
#> 
#> ── Processing Status ──
#> 
#> • Isotope corrected: ✖
#> • ISTD normalized: ✖
#> • ISTD quantitated: ✖
#> • Drift corrected variables: ✖
#> • Batch corrected variables: ✖
#> • Feature filtering applied: ✖
#> 
#> ── Exclusion of Analyses and Features ──
#> 
#> • Analyses manually excluded (`analysis_id`): NA