clustering {MoleculeNetworking} R Documentation

Do spectrum clustering on a small bundle of the ms2 spectrum from a single raw data file

Description

Usage

clustering(ions,
    mzdiff1 = "da:0.1",
    mzdiff2 = "da:0.3",
    intocutoff = 0.05,
    tree.identical = 0.8,
    tree.right = 0.01);

Arguments

ions

-

mzdiff1

the mzdiff tolerance value for group the ms2 spectrum via the precursor m/z, for precursor m/z comes from the ms1 deconvolution peaktable, tolerance error should be smaller in ppm unit; for precursor m/z comes from the ms2 parent ion m/z, tolerance error should be larger in da unit.

mzdiff2

the mzdiff tolerance value for do ms2 peak centroid or peak matches for do the cos similarity score evaluation, should be larger tolerance value in unit da, value of this tolerance parameter could be da:0.3

intocutoff

intensity cutoff value for make spectrum centroid. [as double]

tree.identical

score cutoff for assert that spectrum in the binary tree is in the same cluster node. [as double]

tree.right

score cutoff for assert that spectrum in the binary tree should be put into the right node. [as double]

env

[as Environment]

Details

this workflow usually used for processing the ms2 spectrum inside a single raw data file

Authors

BioNovoGene

Value

this function returns data object of type list. the list data also has some specificied data fields: list(graph, clusters, matrix, cluster.raw).

clr value class

Examples

[Package MoleculeNetworking version 1.0.0.0 Index]