computeRunningMedians {Ringo}R Documentation

Function to compute running medians on a tiling expression set

Description

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

Usage

computeRunningMedians(xSet, probeAnno, modColumn = "Cy5",
allChr = c(1:19, "X", "Y"), winHalfSize = 400, min.probes = 5,
quant = 0.5, combineReplicates = FALSE, 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
modColumn Column of the ExpressionSet's phenoData holding the samples' difference of interest
allChr Character vector of all chromosomes in genome
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
verbose logical; detailed progress output to STDOUT?

Value

An object of class ExpressionSet, holding smoothed intensity values for the probes of the supplied ExpressionSet. The number of results samples is the number of levels in the supplied modColumn of the supplied ExpressionSet's phenoData.

Author(s)

Joern Toedling toedling@ebi.ac.uk

See Also

ExpressionSet, sliding.quantile

Examples

  exDir <- system.file("exData",package="Ringo")
  load(file.path(exDir,"exampleProbeAnno.rda"))
  load(file.path(exDir,"exampleX.rda"))
  smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
modColumn = "Cy5", allChr = c("9"), winHalfSize = 400, verbose = TRUE)
  if (interactive()){
   par(mfrow=c(1,1))
   chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000), ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)
   chipAlongChrom(smoothX, chrom="9", xlim=c(34318000,34321000),
probeAnno=exProbeAnno, itype="l", ilwd=4, paletteName="Spectral",
add=TRUE)
  }

[Package Ringo version 1.2.0 Index]