Import Agilent MassHunter Quantitative Analysis CSV files

Imports .csv files exported from Agilent MassHunter Quantitative Analysis software, containing peak integration results. The input files must have analyses (samples) in rows, features/compounds in columns, and either peak areas, peak heights, or response as the values. Additional columns, such as retention time (RT), full-width at half-maximum (FWHM), precursor m/z (PrecursorMZ), and collision energy (CE), will also be imported and made available in the MRMhubExperiment object for downstream analyses.

When a directory path is provided, all matching .csv 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_masshunter(
  data = NULL,
  path,
  import_metadata = TRUE,
  expand_qualifier_names = TRUE,
  conc_column = "conc_final",
  silent = FALSE
)

Arguments

data

MRMhubExperiment 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 extract and add metadata from the analysis result file

expand_qualifier_names

Logical, whether to add the quantifier name in front of the qualifier name (the latter only has the m/z transition values)

conc_column

Which concentration field of the masshunter data to use, in case "Calc. Conc." and "Final Conc" are present. Default is "conc_final". Must be one of "conc_calc" or "conc_final" (default).

silent

Logical, whether to suppress most notifications

Value

MRMhubExperiment object with the imported data

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 = TRUE,
  expand_qualifier_names = TRUE)
#> ✔ Imported 38 analyses with 31 features.
#> ℹ feature_area selected as default feature intensity. Modify with `set_intensity_var()`.
#> ✔ Analysis metadata associated with 38 analyses.
#> ✔ Feature metadata associated with 31 features.

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