createSimilarityMatrix {MetCirc} | R Documentation |
Creates the similarity matrix by calculating the normalised dot product (NDP) between precursors
createSimilarityMatrix(mm, m = 0.5, n = 2)
mm |
|
m |
|
n |
|
createSimilarityMatrix calls a function to calculate the
NDP between all precursors in the data set. For further
information on how the NDP is calculated see ?NDP
and Li et al. (2015):
Navigating natural variation in herbivory-induced secondary metabolism in
coyote tobacco populations using MS/MS structural analysis. PNAS,
E4147–E4155. Currently m = 0.5
and n = 2
are set as
default.
createSimilarityMatrix
returns a similarity matrix that
contains the NDP similarity measure between all precursors in the data set
Thomas Naake, thomasnaake@googlemail.com
data("binnedMSP", package = "MetCirc") ## truncate binnedMSP binnedMSP <- binnedMSP[1:28,] createSimilarityMatrix(binnedMSP, m = 0.5, n = 2)