msp2TrainingMatrix: msp to Fragmentation Spectra DataBase (FSDB)

In IDSL.FSA: Fragmentation Spectra Analysis (FSA)

msp to Fragmentation Spectra DataBase (FSDB)

Description

This function creates an aligned table from the spectra in the .msp file

Usage

msp2TrainingMatrix(path, MSPfile = "", minDetectionFreq = 1,
selectedFSdbIDs = NULL, dimension = "wide", massAccuracy = 0.01,
allowedNominalMass = FALSE, allowedWeightedSpectralEntropy = TRUE,
noiseRemovalRatio = 0.01, number_processing_threads = 1)

Arguments

path	Address of .msp file or an FSDB
MSPfile	A .msp file name or FSDB in .Rdata format
minDetectionFreq	A minimum detection frequency for an ion across the entire spectra
selectedFSdbIDs	selected MSP block/FSDB IDs to limit the screening to specific ion blocks
dimension	c("wide", "long"). *wide* or *long* alignment matrix output
massAccuracy	A mass accuracy (Da)
allowedNominalMass	c(TRUE, FALSE). Select 'TRUE' only for nominal mass analysis.
allowedWeightedSpectralEntropy	c(TRUE, FALSE). Weighted entropy to transform low abundant signals prior to calculating entropy similarity score. Please see the reference for details on wight transformation.
noiseRemovalRatio	noise removal ratio ([0 - 1])relative to the basepeak to measure entropy similarity score.
number_processing_threads	Number of processing threads for multi-threaded processing

Value

A FSDB file (.Rdata) and aligned spectra table (.csv) are stored in the same directory.

Examples

temp_wd <- tempdir() # just a temporary folder
path_extdata <- system.file("extdata", package = "IDSL.FSA")
MSPfile <- "Kynurenine_Kynurenic_acid.msp"
file.copy(from = paste0(path_extdata, "/", MSPfile), to = temp_wd)
msp2TrainingMatrix(path = temp_wd, MSPfile, minDetectionFreq = 1)

IDSL.FSA documentation built on July 9, 2023, 6:45 p.m.