computeSlidingT {Ringo} | R Documentation

## Function to compute sliding T statistics on a tiling expression set

### Description

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

### Usage

    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)

### Arguments

`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?

### Value

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`.

### Author(s)

Joern Toedling

### See Also

`sliding.meansd`

### Examples

     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")
      }

[Package Ringo version 1.58.0 Index]