tilingArray (version 1.50.0)

segChrom: Fit a piecewise constant curve to along chromosome data (wrapper function)

Description

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.

Usage

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

Arguments

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.

Value

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.

Details

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.

Examples

## 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)