addBackground: Add background for a simulated 4C-seq sample
In walter-ca/Basic4CSim: Basic4CSim: Simulation of 4C-seq data

Description Usage Arguments Value Author(s) Examples

This helper function adds background noise to an empty 4C-seq sample. If the virtual fragment library of the 4C-seq sample does already include counts, those may be overwritten.

1 2	addBackground(simTable, vpStart, powerlawAlpha = 1.35, imRegionDist = 1000000, bgFragCov = 0.01, imFragCov = 0.8, maxFragBG = 1000, maxFragIM = 1500)

`simTable`	virtual simulation fragment library (should be empty)
`vpStart`	position of the experiment's viewpoint
`powerlawAlpha`	alpha for powerlaw background distribution (default: 1.35)
`imRegionDist`	length of intermediate region between viewpoint and far-cis region
`bgFragCov`	coverage rate per fragment for background region fragments (typically low)
`imFragCov`	coverage rate per fragment for intermediate region fragments
`maxFragBG`	maximum signal strength / read number for background fragments
`maxFragIM`	maximum signal strength / read number for fragments in the intermediate region between viewpoint and pure background

Data frame with background reads

Carolin Walter

    if(interactive()) {
        simLibFile <- system.file("extdata", "simLib_short.csv", 
            package="Basic4CSim")
        # load virtual simulation fragment library
        simLib = read.csv(simLibFile, sep = "\t", header = TRUE)
        vpStart = 69999869
        # create empty simulation fragment count table
        simTable = data.frame(simLib[,1:3], "readsL" = 0, "readsR" = 0, 
            simLib[,c(5,9,10)])
        colnames(simTable) = c("chromosomeName", "start", "end", 
            "readsL", "readsR", "isNonBlind", "leftFragEndValid", "rightFragEndValid")
        # add actual background
        set.seed(42)
        simTable = addBackground(simTable, vpStart)
        head(simTable)
    }