| molecular_formula_annotator {IDSL.UFA} | R Documentation |
Molecular Formula Annotator
Description
This module annotates candidate molecular formulas in the peaklists from the IDSL.IPA pipeline using isotopic profiles.
Usage
molecular_formula_annotator(IPDB, spectraList, peaklist, selectedIPApeaks,
massAccuracy, maxNEME, minPCS, minNDCS, minRCS, scoreCoefficients, RTtolerance = NA,
correctedRTpeaklist = NULL, exportSpectraParameters = NULL, number_processing_threads = 1)
Arguments
IPDB |
An isotopic profile database produced by the IDSL.UFA functions. |
spectraList |
a list of mass spectra in each chromatogram scan. |
peaklist |
Peaklist from the IDSL.IPA pipeline |
selectedIPApeaks |
selected IPA peaklist |
massAccuracy |
Mass accuracy in Da |
maxNEME |
Maximum value for Normalized Euclidean Mass Error (NEME) in mDa |
minPCS |
Minimum value for Profile Cosine Similarity (PCS) |
minNDCS |
Minimum value for Number of Detected Chromatogram Scans (NDCS) |
minRCS |
Minimum value for Ratio of Chromatogram Scans (RCS) in percentage |
scoreCoefficients |
A vector of five numbers representing coefficients of the identification score |
RTtolerance |
Retention time tolerance (min) |
correctedRTpeaklist |
corrected retention time peaklist |
exportSpectraParameters |
Parameters for export MS/MS match figures |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A dataframe of candidate molecular formulas