Description Usage Arguments Value References See Also
View source: R/getPersistence.R
Takes a vector
of numeric gene expression over time and computes the persistence score.
The specified lag is used to transform the expression into a 3-D embedded space via time-delay embedding.
A non-linear dimension reduction technique (laplacian eigenmaps) is used to transfrom the 3-D embedding to a 2-D embedding.
Finally, the persistence score of the 2-D embedding is calculated via persistence homology.
Returns the Max persistence score, returns 0 if no persistence score exists.
For more details see TimeCycle's vignette:
vignette("TimeCycle")
.
1 | getPersistence(timeSeries, lag, laplacian = T)
|
timeSeries |
a |
lag |
a |
laplacian |
a |
the max persistence score at the specified lag, returns 0 if no persistence score exists.
Wadhwa RR, Williamson DFK, Dhawan A, Scott JG. (2018). "TDAstats: R pipeline for computing persistent homology in topological data analysis." Journal of Open Source Software. 2018; 3(28): 860. doi:[10.21105/joss.00860]
Bauer U. (2019). "Ripser: Efficient computation of Vietoris-Rips persistence barcodes." arXiv: 1908.02518.
calculate_homology
for Persistence Homology calculation.
buildTakens_ndim
for for generating time-delay embedding.
computeLaplacianEmbedding
for 3-D to 2-D laplacian eigenmaps dimension reduction.
computePersistence
for use parallelized function for a data.frame
of gene expression.
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