segment {tilingArray} | R Documentation |
The function fits a piecewise constant curve to one or multiple sequences of measurements, using a least squares cost function and an O(n) dynamic programming algorithm (see references).
segment(y, maxseg, maxk)
y |
Numeric matrix. Rows correspond to the
x -variable, columns to replicate measurements at the same
value of x . Breakpoints are fitted along the x -axis.
For example, the x -variable can be genomic coordinates or
time. The segmentation will be along the rows of y . |
maxseg |
integer of length 1, maximum number of segments (= 1 + maximum number of change points). |
maxk |
integer of length 1, maximum length of a single segment. |
The complexity of the algorithm is
length(x)*maxk
in memory and
length(x)*maxk*maxcp
in time.
An object of class segmentation
.
W. Huber huber@ebi.ac.uk
[1] Transcript mapping with high-density oligonucleotide tiling arrays. Huber W, Toedling J, Steinmetz, L. Bioinformatics 22, 1963-1970 (2006).
[2] A statistical approach for CGH microarray data analysis. Franck Picard, Stephane Robin, Marc Lavielle, Christian Vaisse, Gilles Celeux, Jean-Jacques Daudin. BMC Bioinformatics. 2005 Feb 11; 6:27.
x = rep( sin((0:4)/2*pi), each=3) + rnorm(3*5, sd=0.1) res = segment(x, maxseg=6, maxk=15)