segChrom {tilingArray} | R Documentation

## Fit a piecewise constant curve to along chromosome data

### Description

This function calls the `segment` function for each strand of one or more chromosomes specified by the user.

### Usage

    segChrom(y, probeAnno, chr=1, nsegs, nrBasesPerSegment = 1500,
                 step=7, confint=FALSE, confintLevel=0.95, save=FALSE, savedir=NULL)

### Arguments

`y` | ExpressionSet or matrix containing the data to be segmented.
`probeAnno` | environment with probe annotations. See package `davidTiling` for an example (?probeAnno).
`chr` | integer scalar or vector specifying which chromosome(s) to segment.
`nsegs` | integer vector specifying the maximum number of segments (= 1 + maximum number of change points) for each chromosome and strand. If missing, this value is calculated by dividing the number of bases on a chromosome by `nrBasesPerSegment`.
`nrBasesPerSegment` | integer (length 1): maximum length of a segment.
`step` | integer, indicating the minimum distance between the 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. Otherwise (`FALSE`), no confidence intervals are returned.
`confintLevel` | numeric scalar between 0 and 1 indicating the probability level for the confidence intervals calculated for each change-point.
`save` | logical scalar. If `TRUE` the results of each segmentation are saved to file in the `savedir` directory. If `FALSE` (default), the results are not saved to file.
`savedir` | optional character string specifying the filepath where the segmentation results will be saved. Only used when `save=TRUE`. Defaults to current working directory.

### Details

This function is a wrapper for the `segment` function which fits piecewise constant curves to along chromosome data. It calls `segment` for each strand of the chromosomes specified by the `chr` argument. Refer to the `segment` help page for further details.

### Value

An environment with containing S4 objects of class `"segmentation"` called "1.+", "1.-", etc (depending on `chr`), where "+" and "-" indicates the strand and the preceding number refers to the chromosome number. If `save=TRUE`, a series of files, "1.+.rda", "1.-.rda", etc (depending on `chr`) are saved in the directory specified.

### Author(s)

Matt Ritchie <ritchie@ebi.ac.uk> and Wolfgang Huber <huber@ebi.ac.uk>

### Examples

    ## library("davidTiling")
    ## data("davidTiling")
    ## data("probeAnno")
    ## isDNA = seq(1:3)
    ## yn = normalizeByReference(davidTiling[,-isDNA],davidTiling[,isDNA], probeAnno=probeAnno)
    ## seg1 = segChrom(yn, probeAnno, chr=1) # this will take a while to run!

[Package tilingArray version 1.12.0 Index]