| FSdb2precursorType {IDSL.FSA} | R Documentation |
Precursor Types from Fragmentation Spectra DataBase (FSDB)
Description
This function finds potential ionization pathways for molecular formulas using a vector of InChIKey values from an FSDB. This function only searches for the first 14 InChIKey letters; and therefore, may result with multiple potential precursor types.
Usage
FSdb2precursorType(InChIKeyVector, libFSdb, tableIndicator = "Frequency",
number_processing_threads = 1)
Arguments
InChIKeyVector |
A vector of InChIKey values. This value may contain whole InChIKey strings or first 14 InChIKey letters. |
libFSdb |
A converted MSP library reference file using the 'msp2FSdb' module which is an FSDB produced by the IDSL.FSA package. |
tableIndicator |
c("Frequency", "PrecursorMZ"). To show frequency or a median of 'PrecursorMZ' values in the output dataframe for each precursor type. |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A matrix of frequency for each InChIKey in the FSDB. The matrix column headers represent precursor types.
Examples
address_input_msp <- system.file("extdata", package = "IDSL.FSA")
MSPfile_vector <- c("Kynurenine_Kynurenic_acid.msp")
libFSdb <- msp2FSdb(path = address_input_msp, MSPfile_vector)
##
InChIKeyVector <- c("HCZHHEIFKROPDY-UHFFFAOYSA-N", "YGPSJZOEDVAXAB-QMMMGPOBSA-N")
precursor_type_table <- FSdb2precursorType(InChIKeyVector, libFSdb,
tableIndicator = "Frequency", number_processing_threads = 1)