segment: Fit a piecewise constant curve: segmentation by dynamic...

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

Description

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).

Usage

segment(y, maxseg, maxk)

Arguments

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.

Details

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

Value

An object of class segmentation.

Author(s)

W. Huber [e-mail]

References

[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.

Examples

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

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: pixmap
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

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