ms2Group: group MS/MS precursor masses

In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

Description

hierarchically cluster ms/ms precursor scans within and across samples, according to a m/z and retention time error.

Usage

ms2Group(adductSpectra = NULL, nCores = NULL, 
maxRtDrift = NULL, 
ms1mzError = 0.1, ms2mzError = 1, dotProdClust = TRUE, minDotProd = 0.8,
fclustMethod = "median", disMetric = "euclidean", compSpecGen = TRUE,
adjPrecursorMZ = TRUE)

Arguments

adductSpectra	AdductSpec object
nCores	numeric the number of cores to use for parallel computation. The default is to use 1 core.
maxRtDrift	numeric for the maximum rentention time drift to be considered. Default is 20.
ms1mzError	numeric maximum MS1 mass:charge error
ms2mzError	numeric maximum MS2 mass:charge error
dotProdClust	logical remove previous dot prod clustering results
minDotProd	numeric. Minimum mean dot product spectral similarity score to keep a spectrum within an MS/MS group (default = 0.8).
fclustMethod	method to use for the fclust function
disMetric	metric to use for distance in clustering
compSpecGen	logical for whether composite spectra generation is necessary
adjPrecursorMZ	logical for precursor mass:charge adjustment

Value

a list identical to adductSpectra containing an additional list element:

JosieLHayes/adductomicsR documentation built on May 5, 2019, 9:43 p.m.