computeRunningMedians: Function to compute running medians on a tiling expression...
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Value Author(s) See Also Examples

Function to compute running medians (or other quantiles) on a tiling expression set.

computeRunningMedians(xSet, probeAnno, modColumn = "Cy5",
 allChr, winHalfSize = 400, min.probes = 5, quant = 0.5,
 combineReplicates = FALSE, nameSuffix = ".sm", checkUnique=TRUE,
 uniqueCodes=c(0), verbose = TRUE)

`xSet`	Object of class `ExpressionSet` holding the normalized probe intensity data
`probeAnno`	Environment holding the genomic positions of probes in the ExpressionSet
`modColumn`	Column of the ExpressionSet's `phenoData` holding the samples' difference of interest
`allChr`	Character vector of all chromosomes in genome; if not specified (defaul) all chromosomes annotated in the supplied `probeAnno` are used.
`winHalfSize`	Half the size of the window centered at a probe position, in which all other probes contribute to the calculation of the median.
`min.probes`	integer; if less probes are in the sliding window, NA instead of the median is returned. This meant to avoid to computing non-meaningful medians. If unwanted, set this to 1 or less
`quant`	numeric; which quantile to use for the smoothing. The default `0.5` means compute the median over the values in the sliding window.
`combineReplicates`	logical; should the median not be computed over individual samples in the ExpressionSet, but should samples be combined according to the column `modColumn` of the `phenoData`. The median is then computed across all probe levels and samples of the same type in the window. The resulting ExpressionSet has so many columns as are there different entries in the column `modColumn`
`nameSuffix`	character; suffix attached to the sample labels of the supplied ExpressionSet `xSet` for the sample names of the resulting ExpressionSet.
`checkUnique`	logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used.
`uniqueCodes`	numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness?
`verbose`	logical; detailed progress output to STDOUT?

An object of class ExpressionSet, holding smoothed intensity values for the probes of the supplied ExpressionSet. The number of results samples is either the number of levels in the supplied modColumn of the supplied ExpressionSet's phenoData if combineReplicates is set to TRUE or equal to the number of samples in the supplied ExpressionSet xSet otherwise.

Joern Toedling

ExpressionSet, sliding.quantile, probeAnno-class

  exDir <- system.file("exData",package="Ringo")
  load(file.path(exDir,"exampleProbeAnno.rda"))
  load(file.path(exDir,"exampleX.rda"))
  smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
                                   winHalfSize = 400)
  combX <- combine(exampleX, smoothX)
  if (interactive()){
   grid.newpage()
   plot(combX, exProbeAnno, chrom="9", xlim=c(34318000,34321000),
        ylim=c(-2,4), gff=exGFF)
  }