addOffset {qsea} | R Documentation |
This function sets the background reads offset parameters for the qseaSet object, either by estimating offset reads, or by setting user provided values.
addOffset(qs,enrichmentPattern , maxPatternDensity=0.01,offset)
qs |
the qseaSet object |
enrichmentPattern |
name of the enrichment pattern, as specified in addPatternDensity |
maxPatternDensity |
Maximum pattern density, at which the window is treated as pattern free. |
offset |
This parameter alternatively allows to specify the amount of background reads for each sample manually. In this case, please provide average background reads for CNV free windows in rpkm scale. |
The function returns the qseaSet object, extended by the estimated amount of background reads for all samples
Mathias Lienhard
addPatternDensity, getOffset
#simulate data with varing background fractions qs=getExampleQseaSet(expSamplingDepth=5e4, repl=5,bgfraction=seq(0,.8,.2)) #estimate the background in simulated data addOffset(qs, "CpG", maxPatternDensity=0.7) #return the background on different scales getOffset(qs, scale="fraction") #estimated fraction of total reads getOffset(qs, scale="rpw") #average background reads per CNV free window