Import compound and spectrum information from MoNa

import_mona_sdf() allows to import compound and spectrum information from an SDF file from MoNa (Massbank of North America http://mona.fiehnlab.ucdavis.edu/). This function is a convenience function using the compound_tbl_sdf() and msms_spectra_mona() functions for data import but avoiding to read the SDF files twice.

Usage

import_mona_sdf(x, nonStop = TRUE)

Arguments

x

character(1) being the SDF file name.

nonStop

logical(1) whether file content specific errors should only reported as warnings and not break the full import process. The value of this parameter is passed to parameter skipErrors of the read.SDFset() function.

Value

A list with elements "compound" and "msms_spectrum" containing data.frames with compound and MS/MS spectrum data, respectively.

Note

MoNa SDF files organize the data by individual spectra (i.e. each element is one spectrum) and individual compounds can not easily and consistently defined (i.e. not all entries have an InChI ID or other means to uniquely identify compounds). Thus, the function returns a highly redundant compound table. Feedback on how to reduce this redundancy would be highly welcome!

See also

compound_tbl_sdf() to read only the compound information.

msms_spectra_mona() to read only the spectrum data.

Author

Johannes Rainer

Examples

## Define the test file containing a small subset from MoNa
fl <- system.file("sdf/MoNa_export-All_Spectra_sub.sdf.gz",
    package = "CompoundDb")

## Import the data
res <- import_mona_sdf(fl)
#> Reading SDF file ... 
#> OK
#> Extracting compound information ... 
#> Warning: MoNa data can currently not be normalized and the compound table contains thus highly redundant data.
#> OK
#> Extracting spectrum information ... 
#> OK