segChrom: Fit a piecewise constant curve to along chromosome data...
In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description Usage Arguments Details Value Author(s) Examples

Wrapper around the segment function for each strand of one or more chromosomes specified by the user. It does some typical preprocessing and I/O.

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segChrom(y, probeAnno, chr=1:17, strands=c("+", "-"), 
  nrBasesPerSegment = 1500, maxk = 3000, step = 7, confint = FALSE,
  confintLevel = 0.95, useLocks=TRUE, verbose=TRUE, savedir)

`y`	ExpressionSet or matrix containing the data to be segmented.
`probeAnno`	an object of class `probeAnno` (defined in the Ringo package) or an environment with probe annotations. For the latter, see the package `davidTiling` for an example (?probeAnno).
`chr`	integer scalar or vector specifying which chromosome(s) to segment.
`strands`	character scalar or vector specifying which strands to segment; can also be `NA`.
`nrBasesPerSegment`	integer (length 1): the parameter `maxseg` of the `segment` function is calculated as the length of the chromosome divided by `nrBasesPerSegment`. Thus, it determines the average segment length in the finest segmentation.
`maxk`	passed on to the function `segment`.
`step`	integer scalar, indicating the minimum distance between consecutive probes. In cases when probes are offset by less than `step` bases, the probes are sampled to achieve the desired spacing.
`confint`	logical scalar. If `TRUE`, confidence intervals for each change-point are calculated.
`confintLevel`	numeric scalar between 0 and 1 indicating the probability level for the confidence intervals that are calculated for each change-point.
`useLocks`	logical scalar. Should a file locking mechanism be used that allows for a simple-minded parallelization of this function.
`verbose`	logical scalar. Should we be chatty about our progress?
`savedir`	character scalar. If specified, resulting `segmentation` objects are saved (with `save`) to this directory.

This function is a wrapper for the segment function. It is provided in this package for illustration. For applications to different datasets, you will likely need to adapt it to some extent, please refer to its source code.

An environment containing S4 objects of class "segmentation" called "1.+", "1.-", etc. (depending on the values in chr and strands), where "+" and "-" indicate the strand and the preceding number refers to the chromosome. If savedir is specified, there is also the side-effect that a series of files "1.+.rda", "1.-.rda", etc. is saved in that directory.

Wolfgang Huber <whuber@embl.de>

## Not run: 
  library("davidTiling")
  data("davidTiling")
  data("probeAnno")
  isDNA = seq(1:3)
  yn = normalizeByReference(davidTiling[,-isDNA],davidTiling[,isDNA], probeAnno=probeAnno)
  seg = segChrom(yn, probeAnno) ## this will take a while to run!

## End(Not run)