Main Function

TimeCycle()

Main TimeCycle Function

Example Data

zhang2014

Example data set of normalized microarray time-series expression set from Zhang et. al. of WT mouse liver sampled every 2-h for 48-h

Internal Helper Functions

averageReps()

Handles Sample Replicates in Single Time-Series

buildTakens_ndim()

Generates Takens' Embedding For a Time-Series

computeLaplacianEmbedding()

Computes the Laplacian Eigenmap For Dimension Reduction

computePersistence()

Computes Persistence Scores For a Data.Frame of Time-Series Across Multiple Lags

detrend()

Linearly Detrends a data.frame of Gene Expression Time-Series

getFFT()

Computes the Fast Fourier Transform of a Time-Series

getPersistence()

Computes Persistence Scores For a Single Time-Series Across a Single Lag

getRepAvgedDataFrame()

Handles Sample Replicates in a data.frame of Time-Series

getTimeSpan()

Computes Algorithm Run Time

imputeMissingData()

Imputates Missing Time-Points in Data

matrixLaplacian()

Computes Laplacian Eigenmaping

meanCenter()

Mean Centers a data.frame

movingAverage()

Computes the Moving Average of a Single Time-Series

movingAverageDF()

Computes the Moving Average By Row in a data.frame of Time-Series

nullResampling()

Generates a data.frame of Resampled Time-Series for Computing the Null Distribution

periodFinder()

Estimates the period, amp, and phase of a data.frame of time-series

preprocess_acf()

Computes Time-Series Autocovariance Function

resampleTimeSeries()

Generates a data.frame of Resampled Time-Series

scaleTimeSeries()

Scales a Time-Series