segChrom {tilingArray} | R Documentation |
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.
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 |
environment with probe annotations. See
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. |
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.
Refer to its help page for further details.
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.
Matt Ritchie <ritchie@ebi.ac.uk> and Wolfgang Huber <huber@ebi.ac.uk>
## 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)