neutralloss {MetCirc} | R Documentation |
Calculate similarity based on neutral losses (NLS)
neutralloss(x, y, m=0.5, n=2, ...)
x |
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y |
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m |
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n |
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... |
further arguments passed to MSnbase:::bin_Spectra |
Similarities of spectra based on neutral losses are calculated according to the following formula:
∑(W_{S1, i} \cdot W_{S2, i}) ^ 2 ∑(W_{S1, i} ^ 2) * ∑(W_{S2, i} ^ 2)
,
with W = [ peak intensity] ^{m} \cdot [ NL ]^n and
NL = | m/z - precursor m/z |. For further information
see Li et al. (2015): Navigating natural variation in herbivory-induced
secondary metabolism in coyote tobacco populations using MS/MS structural
analysis. PNAS, E4147–E4155. neutralloss
returns a numeric
value ranging between 0 and 1, where 0
indicates no similarity between the two MS/MS features, while 1 indicates
that the MS/MS features are identical. Arguments can be passed to
the function MSnbase:::bin_Spectra
, e.g. to set the width of bins
(binSize).
Prior to calculating
W_{S1}
or
W_{S2}
, all intensity values are divided by the maximum intensity value.
neutralloss returns a numeric similarity coefficient between 0 and 1
Thomas Naake, thomasnaake@googlemail.com
data("spectra", package = "MetCirc") x <- spectra_tissue[[1]] y <- spectra_tissue[[2]] neutralloss(x, y, m=0.5, n=2, binSize=0.01)