Description Usage Arguments Value Examples
Compute low-dimensional representation of dataset.
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Y |
\[N x P\] data matrix for which the dimensionality of P should be reduced |
method |
Dimensionality reduction method [character] to be applied; one of DiffusionsMaps, DRR, ICA, LLE, Isomap, LaplacianEigenmap, MDS, PCA, kPCA, nMDS, tSNE and UMAP. |
optN |
optimal number [integer] of neighbours to consider for
dimensionality reduction; relevant for methods LLE, LaplacianEigenmaps,
Isomap and tSNE. If not provided, will be estimated via
|
ndim |
maximum dimensionality [integer] to retain in the data; large values can cause long computation times; if not provided max(P,N) is chosen. |
kmin |
if optN is not provided, kmin [integer] specifies the minimum
number of neighbours supplied to |
kmax |
if optN is not provided, kmax [integer] specifies the maximum
number of neighbours supplied to |
verbose |
[logical] If set, progress messages are printed to standard out. |
parallel |
[logical] if optN is not provided and parallel TRUE, parallel
computation on multiple cpu cores is used with |
is.list.ellipsis |
[logical] if ... arguments are provided as list, set TRUE. |
... |
Additional arguments passed to dimensionality reduction methods. For possible arguments, check function decomentation. See details for relevant packages and functions. |
named list of results from dimensionality reduction: Y_red: named list with dimensionality reduced phenotypes (reducedY) and object returned by specified dimensionality reduction method (results) with additional output M: vector [double] with Trustworthiness and Continuity estimates for the dimensionality reduction
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