FSA_uniqueMSPblockTagger: FSA Unique MSP Block Tagger

In IDSL.FSA: Fragmentation Spectra Analysis (FSA)

FSA Unique MSP Block Tagger

Description

This function removes similar MSP blocks. This function aggregates MSP blocks based on the 'Name' values.

Usage

FSA_uniqueMSPblockTagger(path, MSPfile = "", aggregateBy = "Name",
massError = 0.01, RTtolerance = NA, minEntropySimilarity = 0.75,
noiseRemovalRatio = 0.01, allowedNominalMass = FALSE,
allowedWeightedSpectralEntropy = TRUE, plotSpectra = FALSE,
number_processing_threads = 1)

Arguments

path	Address of .msp file or an FSDB
MSPfile	name of .msp file
aggregateBy	a variable to aggregate the MSP blocks based on
massError	Mass accuracy in Da
RTtolerance	Retention time tolerance (min) to match msp blocks. Select NA to ignore retention time match.
minEntropySimilarity	Minimum entropy similarity score
noiseRemovalRatio	noise removal ratio relative to the basepeak to measure entropy similarity score (in percent)
allowedNominalMass	c(TRUE, FALSE). Select 'TRUE' only for nominal mass analysis.
allowedWeightedSpectralEntropy	c(TRUE, FALSE). Weighted entropy to measure entropy similarity score.
plotSpectra	c(TRUE, FALSE)
number_processing_threads	Number of processing threads for multi-threaded processing

Value

a list of similar MSP blocks is returned at the end and a subsetted .msp and FSDB files are saved in the 'path' directory.

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