Imports a .csv file with Agilent MassHunter Quantitative Analysis results.
Samples should be in rows, features/compounds in columns and must contain either peak areas, peak heights or intensities.
Additional columns, such as RT (rentention time), FWHM, PrecursorMZ, and CE will be imported and available from the MidarExperiment object for downstream analyses.
When more than one file is provided, all files are imported and merged into one raw dataset. This can be useful, e.g. when importing datasets that are pre-processing in blocks resulting in different files. Each Datafile/Feature pair needs to be unique within and across data files, presense of replicates return an error.
Arguments
- data
MidarExperiment object
- file_dir_names
One or more file names with path or folder path. When a folder name is given, all *.csv files in this folder will be read.
Examples
csvfile <- system.file("extdata", "Example_MHQuant_1.csv", package = "midar")
mexp <- MidarExperiment()
mexp <- read_masshunter_csv(mexp, csvfile)
#> Reading [Example_MHQuant_1.csv] ...
#> ✓ Imported 215 samples with 428 transitions.
mexp
#> Warning: Unknown or uninitialised column: `FEATURE_NAME`.
#>
#> MidarExperiment
#>
#> Data:
#> • Samples: 0
#> • Features: 0
#>
#> Metadata:
#> • Sample annotation: ✗
#> • Feature annotation: ✗
#> • Internal standard annotation: ✗
#> • Response curves annotation: ✗
#> • Study samples annotation: ✗
#>
#> Processing status: Raw Data
#>
#> Processing:
#> • ISTD normalized: ✗
#> • ISTD quantitated: ✗
#> • Drift corrected: ✗
#> • Batch corrected: ✗
#> • Interference (isotope) corrected: ✗