ms2Group: group MS/MS precursor masses

Description Usage Arguments Value

View source: R/ms2Group.R

Description

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

Usage

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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:


adductomicsR documentation built on Nov. 8, 2020, 4:49 p.m.