createStructuralAdjacency {MetNet} | R Documentation |
The function createStructuralAdjacency
infers an
adjacency matrix using differences in m/z values that are matched against a
data.frame
of theoretically calculated differences of
loss/addition of functional groups. createStructuralAdjacency
returns
the unweighted adjacency matrix together with a character matrix with the
type of loss/addition as a list at the specific positions.
createStructuralAdjacency(x, transformation, ppm=5)
x |
matrix, where columns are the samples and the rows are features
(metabolites), cell entries are intensity values, |
transformation |
data.frame, containing the columns |
ppm |
numeric, mass accuracy of m/z features in parts per million (ppm) |
createStructuralAdjacency
accesses the column 'mz'
of
x
to infer structural topologies based on the functional groups
supplied by transformation
. To account for the mass accuracy of
the dataset x
, the user can specify the accuracy of m/z features
in parts per million (ppm) by the ppm
argument. The m/z values in the
'mz'
column of x
will be converted to m/z ranges according to
the ppm
argument (default ppm=5
).
list containing two matrices, in the first list entry the
matrix with edges inferred mass differences is stored, in the second list
entry the matrix with the type (corresponding to the "group"
column
in transformation
) is stored
Thomas Naake, thomasnaake@googlemail.com
data("x_test", package="MetNet") transformation <- rbind( c("Hydroxylation (-H)", "O", "15.9949146221"), c("Malonyl group (-H2O)", "C3H2O3", "86.0003939305"), c("C6H10O6", "C6H10O6", "178.0477380536"), c("D-ribose (-H2O) (ribosylation)", "C5H8O4", "132.0422587452"), c("Disaccharide (-H2O)", "C12H20O11", "340.1005614851"), c("Glucuronic acid (-H2O)", "C6H8O6", "176.0320879894"), c("Monosaccharide (-H2O)", "C6H10O5", "162.0528234315"), c("Trisaccharide (-H2O)", "C18H30O15", "486.1584702945")) transformation <- data.frame(group=transformation[,1], formula=transformation[,2], mass=as.numeric(transformation[,3])) struct_adj <- createStructuralAdjacency(x_test, transformation, ppm=5)