Ringo (version 1.36.0)

computeSlidingT: 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.

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")
  }