addEnrichmentParameters: Enrichment analysis
In qsea: IP-seq data analysis and vizualization

Description Usage Arguments Value Author(s) See Also Examples

This function analyses the dependency of enrichment on a sequence pattern, based on a subset of windows for which the signal is known.

1 2	addEnrichmentParameters(qs, enrichmentPattern, signal, windowIdx, min_wd=5,bins=seq(.5,40.5,1))

`qs`	The qseaSet object
`enrichmentPattern`	The name of the pattern, on which the enrichment depends on (usually CpG for methylation analysis). This name must correspond to the name specified in addPatternDensity()
`windowIdx`	vector of window indices, for which "true" values are known (or can be estimated)
`signal`	Matrix containing the known (or estimated) values for all samples and all specified windows, as a numeric matrix. These values are expected to be between 0 and 1.
`bins`	For the enrichment analysis, windows are binned according to pattern density. This parameter specifies the bins.
`min_wd`	minimal number of windows per bin to be considered

The function returns the qseaSet object, extended by the parameters of the enrichment profiles for all samples

Mathias Lienhard

plotEnrichmentProfile, addPatternDensity

qs=getExampleQseaSet(enrichmentAnalysis=FALSE)
#this procedure assumes that regions with low CpG density is 80% methylated
#on average, and regions within CpG islands are 25% methylated on average. 
wd=which(getRegions(qs)$CpG_density>1 &
    getRegions(qs)$CpG_density<15)
signal=(15-getRegions(qs)$CpG_density[wd])*.55/15+.25
signal=matrix(signal,nrow=length(signal),ncol=length(getSampleNames(qs)))
qs=addEnrichmentParameters(qs, enrichmentPattern="CpG", 
    windowIdx=wd, signal=signal)