Imports MRMkit peak integration results

Imports tabular data files (*.tsv) generated from MRMkit containing peak integration results. The input files must be in a long format with columns for the raw data file name, feature ID, peak intensity, and other parameters. Additional information, such as retention time, FWHM, precursor/product MZ, and CE will also be imported and made available in the MidarExperiment object for downstream analyses.

When a directory path is provided, all matching files in that directory will be imported and merged into a single dataset. This is useful when importing datasets that were pre-processed in blocks, resulting in multiple files. Each unique combination of feature and raw data file must only occur once across all source data files. Duplicate combinations will result in an error.

Usage

import_data_mrmkit(data = NULL, path, import_metadata, silent = FALSE)

Arguments

data

MidarExperiment object

path

One or more file paths, or a directory path (in which case all matching files will be imported)

import_metadata

Logical, whether to import additional metadata columns (e.g., batch_id, qc_type)

silent

Logical, whether to suppress most notifications

Value

MidarExperiment object with the imported data

Examples

mexp <- MidarExperiment()

file_path = system.file("extdata", "MRMkit_demo.tsv", package = "midar")

mexp <- import_data_mrmkit(
  data = mexp,
  path = file_path,
  import_metadata = TRUE)
#> ✔ Imported 499 analyses with 28 features
#> ℹ `feature_area` selected as default feature intensity. Modify with `set_intensity_var()`.
#> ✔ Analysis metadata associated with 499 analyses.
#> ✔ Feature metadata associated with 28 features.
print(mexp)
#> 
#> ── MidarExperiment ─────────────────────────────────────────────────────────────
#> Title:
#> 
#> Processing status: Annotated raw AREA values
#> 
#> ── Annotated Raw Data ──
#> 
#> • Analyses: 499
#> • Features: 28
#> • 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