createVirtualFragmentLibrarySimulation: Create a virtual simulation fragment library with two...
In walter-ca/Basic4CSim: Basic4CSim: Simulation of 4C-seq data

Description Usage Arguments Value Author(s) Examples

Basic4CSim adapts Basic4Cseq's createVirtualFragmentLibrary function to provide sequence data for fragment end data simulation.

createVirtualFragmentLibrarySimulation(chosenGenome, firstCutter, secondCutter, 
readLength, onlyNonBlind = TRUE, useOnlyIndex = FALSE, minSize = 0, maxSize = -1, 
minFragEndSize = 0, maxFragEndSize = 10000000, useAllData = TRUE, 
chromosomeName = "chr1", libraryName = "default")

`chosenGenome`	The genome that is to be digested in silico with the provided enzymes; can be an instance of BSgenome or DNAString (Basic4Cseq)
`firstCutter`	First of two restriction enzymes (Basic4Cseq)
`secondCutter`	Second of two restriction enzymes (Basic4Cseq)
`readLength`	Read length for the experiment (Basic4Cseq)
`onlyNonBlind`	Variable that is TRUE (default) if only non-blind fragments are considered (i.e. all blind fragments are removed) (Basic4Cseq)
`useOnlyIndex`	Convenience function to adapt the annotation style of the chromosomes ("chr1", ... "chrY" or "1", ..., "Y"); parameter has to be set to match the BAM file in question (Basic4Cseq)
`minSize`	Filter option that allows to delete fragments below a certain size (in bp) (Basic4Cseq)
`maxSize`	Filter option that allows to delete fragments above a certain size (in bp) (Basic4Cseq)
`minFragEndSize`	Filter option that allows to delete fragment ends below a certain size (in bp) (Basic4Cseq)
`maxFragEndSize`	Filter option that allows to delete fragment ends above a certain size (in bp) (Basic4Cseq)
`useAllData`	Variable that indicates if all data of a BSgenome package is to be used. If FALSE, chromosome names including a "_" are removed, reducing the set of chromosomes to (1 ... 19, X, Y, MT) for the mouse genome or (1 ... 22, X, Y, MT) for the human genome (Basic4Cseq)
`chromosomeName`	Chromosome name for the virtual fragment library if a `DNAString` object is used instead of a `BSgenome` object (Basic4Cseq)
`libraryName`	Name of the file the created virtual fragment library is written to. Per default the file is called "fragments_firstCutter_secondCutter.csv". The fragment data is returned as a data frame if and only if an empty character string is chosen as `libraryName`. (Basic4Cseq)

A tab-separated file with the specified virtual fragment library (cp. Basic4Cseq), with added fragment end sequences

Carolin Walter

    if(interactive()) {
        library(BSgenome.Ecoli.NCBI.20080805)
        fragmentData = createVirtualFragmentLibrarySimulation(chosenGenome = Ecoli$NC_002655, firstCutter = "catg", secondCutter = "gtac", readLength = 30,  onlyNonBlind = TRUE, chromosomeName = "NC_002655", libraryName = "fragments_Ecoli.csv")
    }