compute_sliding_t: Function to compute sliding T statistics on a tiling...
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Value Author(s) See Also Examples

Function to compute sliding (regularized) one- or two-sample T statistics on a tiling expression set.

1	computeSlidingT(xSet, probeAnno, allChr = c(1:19, "X", "Y"), test = "one.sample", grouping = NULL, winHalfSize = 400, min.probes = 5, 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
`allChr`	Character vector of all chromosomes in genome
`test`	character; one of `one.sample` or `two.sample`
`grouping`	factor vector of length equal to number of samples, not required if `test=one.sample`
`winHalfSize`	Half the size of the window centered at a probe position, in which all other probes contribute to the calculation of the mean and standard deviation.
`min.probes`	integer; if less probes are in the sliding window, NA instead of the mean and sd is returned. This is meant to avoid to computing non-meaningful means and standard deviations. If unwanted, set this to 1 or less
`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 the T statistics values for the probes of the supplied ExpressionSet. The number of results samples is the number of levels in the supplied factor grouping.

Joern Toedling

sliding.meansd

 exDir <- system.file("exData",package="Ringo")
  load(file.path(exDir,"exampleProbeAnno.rda"))
  load(file.path(exDir,"exampleX.rda"))
  tX <- computeSlidingT(exampleX, probeAnno=exProbeAnno,
             allChr=c("9"), winHalfSize=400)
  sampleNames(tX) <- "t-Stat_Suz12vsTotal"
  if (interactive()){
    grid.newpage()
    plot(cbind2(exampleX, tX), exProbeAnno, chrom="9",
         xlim=c(34318000,34321000), ylim=c(-2,8.5), gff=exGFF,
         paletteName="Paired")
  }