View source: R/createCompDbPackage.R
import_mona_sdf | R Documentation |
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.
import_mona_sdf(x, nonStop = TRUE)
x |
|
nonStop |
|
A list
with elements "compound"
and "msms_spectrum"
containing
data.frames with compound and MS/MS spectrum data, respectively.
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!
Johannes Rainer
compound_tbl_sdf()
to read only the compound information.
msms_spectra_mona()
to read only the spectrum data.
## 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)
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