addCisPeaks: Add peaks in cis for a simulated 4C-seq sample
In walter-ca/Basic4CSim: Basic4CSim: Simulation of 4C-seq data

Description Usage Arguments Value Author(s)

This helper function adds regions of higher signal (peaks) in cis to a 4C-seq sample. Random noise as well as modifiers for blind fragments can be added. The default shape of peaks resembles a normal distribution, however block shaped peaks can be created as well.

1 2	addCisPeaks(simTable, peaks, minRandomAdd = -500, maxRandomAdd = 500, chanceRandom = 0.8, differenceRandom = 0.2, zeroRate = 0, blindFactor = 0.2, block = FALSE)

`simTable`	virtual simulation fragment library
`peaks`	list of peaks to be simulated: ID (e.g. number), mean (genomic coordinate), max (maximum signal for the peak in question), sd (standard deviation, "width")
`minRandomAdd`	minimum for randomly chosen summand to fragment read count (can be negative)
`maxRandomAdd`	maximum for randomly chosen summand to fragment read count (can be negative)
`chanceRandom`	chance for occurrence of random summands
`differenceRandom`	parameter to manipulate peak heights per peak: (1-dR) <= max <= (1+dR)
`zeroRate`	percentage of fragments in the peak region which are set to 0
`blindFactor`	factor applied to read counts on blind fragments within peak regions
`block`	parameter that determines the shape of simulated peaks (default: normal distribution / bell shape)