findsegments: Fit a piecewise constant curve to a sequence of numbers -...

In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description

This function is only here for backward compatibility - please use segment.

The function fits a piecewise constant curve to a sequence of numbers using a simple least squares cost function and the dynamic programming algorithm described by Picard et al. (see reference).

Usage

findSegments(x, maxcp, maxk, verbose=TRUE)

Arguments

x	Numeric (real) vector.
maxcp	Integer (length 1): maximum number of segments (= 1 + maximum number of change points).
maxk	Integer (length 1): maximum length of a segment.
verbose	Logical: if this parameter has a positive value, various diagnostic output is printed.

Details

The complexity of the algorithm is length(x)*maxk in memory and length(x)*maxk*maxcp in time.

Value

An object of class "segmentation" A list with elements

J	likelihood criterion
th	matrix of segment start points
dat	the data used for the segmentation
call	the function call

.

See the vignette, and the paper cited below for details.

Note

This function is depracated and replaced by function segment, but still included for backward compability.

Author(s)

W. Huber [e-mail], Joern Toedling [e-mail]

References

A statistical approach for CGH microarray data analysis. Franck Picard, Stephane Robin, Marc Lavielle, Christian Vaisse, Gilles Celeux, Jean-Jacques Daudin, Rapport de recherche No. 5139, Mars 2004, Institut National de Recherche en Informatique et en Automatique (INRIA), ISSN 0249-6399. The code of this function is based on the Matlab implementation presented at http://www.inapg.fr/ens_rech/mathinfo/recherche/mathematique/outil.html, but it has evolved.

Examples

 x = rep( sin((0:4)/2*pi), each=3) + rnorm(3*5, sd=0.1)
 res = findSegments(x, maxcp=6, maxk=15)

tilingArray documentation built on Nov. 8, 2020, 10:59 p.m.