Read a MGF file into a tidy tibble — read

MGF files allow the storage of MS/MS spectra. With this function they can be read 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.

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]>