ms2Group {adductomicsR} | R Documentation

## group MS/MS precursor masses

### 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:

[Package adductomicsR version 1.0.0 Index]