Read a MGF file into a tidy tibble — read

MGF files allow the storage of MS/MS spectra. This function reads them into a tidy tibble. Each variable is stored in a column and each ion (observation) is stored in a separate row. MS/MS spectra are stored in a list column named MSn.
Please note that MGF files are software-specific so the variables and their names may vary. This function was developed with the GNPS file format exported from mzmine in mind.

If you encounter any bugs please report them: https://github.com/yasche/metamorphr/issues

Usage

read_mgf(file, show_progress = TRUE)

Arguments

file: The path to the MGF file.
show_progress: A logical indicating whether the progress of the import should be printed to the console. Only important for large MGF files.

Value

A tidy tibble holding MS/MS spectra.

Examples

mgf_path <- system.file("extdata", "toy_mgf.mgf", package = "metamorphr")
read_mgf(mgf_path)
#> # A tibble: 3 × 5
#>   VARIABLEONE VARIABLETWO VARIABLETHREE PEPMASS MSn             
#>         <dbl>       <dbl>         <dbl>   <dbl> <list>          
#> 1         1.1         1.2           1.3    45.7 <tibble [3 × 2]>
#> 2         2.1         2.2           2.3   679.  <tibble [5 × 2]>
#> 3         3.1         3.2           3.3  5890.  <tibble [6 × 2]>