| clustering {MoleculeNetworking} | R Documentation |
clustering(ions,
mzdiff1 = "da:0.1",
mzdiff2 = "da:0.3",
intocutoff = 0.05,
tree.identical = 0.8,
tree.right = 0.01);-
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.
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
intensity cutoff value for make spectrum centroid. [as double]
score cutoff for assert that spectrum in the binary tree is in the same cluster node. [as double]
score cutoff for assert that spectrum in the binary tree should be put into the right node. [as double]
[as Environment]
this workflow usually used for processing the ms2 spectrum inside a single raw data file
list(graph, clusters, matrix, cluster.raw).