dproc2: Modified Procrustes distance

In ICGE: Estimation of Number of Clusters and Identification of Atypical Units

Modified Procrustes distance

Description

dproc2 computes and returns all the pairwise procrustes distances between genes in a time course experiment, using their expression profile.

Usage

dproc2(x, timepoints = NULL)

Arguments

x	a matrix containing, in its rows, the gene expression values at the T considered time points.
timepoints	a T-vector with the T observed time points. If timepoints=NULL (default), then timepoints=1:T.

Details

Each row i of matrix x is arranged in a two column matrix Xi. In Xi, the first column contains the time points and the second column the observed gene expression values (xi1...).

Value

A dist object with distance information.

Author(s)

Itziar Irigoien [e-mail]; Konputazio Zientziak eta Adimen Artifiziala, Euskal Herriko Unibertsitatea (UPV/EHU), Donostia, Spain.

Conchita Arenas [e-mail]; Departament d'Estadistica, Universitat de Barcelona, Barcelona, Spain.

References

Irigoien, I. , Vives, S. and Arenas, C. (2011). Microarray Time Course Experiments: Finding Profiles. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2), 464–475.

Gower, J. C. and Dijksterhuis, G. B. (2004) Procrustes Problems. Oxford University Press.

Sibson, R. (1978). Studies in the Robustness of Multidimensional Scaling: Procrustes statistic. Journal of the Royal Statistical Society, Series B, 40, 234–238.

See Also

dist, dmahal, dgower, dcor dbhatta

Examples

# Given  10  hypothetical time course profiles
# over 6 time points at 1, 2, ..., 6 hours.
x <- matrix(c(0.38, 0.39, 0.38, 0.37, 0.385, 0.375,
              0.99, 1.19, 1.50, 1.83, 2.140, 2.770,
              0.38, 0.50, 0.71, 0.72, 0.980, 1.010,
              0.20, 0.40, 0.70, 1.06, 2.000, 2.500,
              0.90, 0.95, 0.97, 1.50, 2.500, 2.990,
              0.64, 2.61, 1.51, 1.34, 1.330 ,1.140,
              0.71, 1.82, 2.28, 1.72, 1.490, 1.060,
              0.71, 1.82, 2.28, 1.99, 1.975, 1.965,
              0.49, 0.78, 1.00, 1.27, 0.590, 0.340,
              0.71,1.00, 1.50, 1.75, 2.090, 1.380), nrow=10, byrow=TRUE)

# Graphical representation
matplot(t(x), type="b")

# Distance matrix between them
d <- dproc2(x)

ICGE documentation built on Oct. 17, 2022, 5:10 p.m.