printFastq: Add random near-cis peaks to a simulated 4C-seq sample
In walter-ca/Basic4CSim: Basic4CSim: Simulation of 4C-seq data

Description Usage Arguments Value Author(s) Examples

This function collects actual sequence data per fragment for a simulated 4C-seq sample (in a fragment table format), and exports them with a high quality score per read as a fastq file.

1	printFastq(simTable, simLib, ID, firstCutter, lengthRead = 26)

`simTable`	virtual simulation fragment library with fragment read counts representing a simulated 4C-seq sample
`simLib`	original virtual simulation fragment library, with fragment end sequences for simulation purposes
`ID`	sample name
`firstCutter`	first restriction enzyme sequence
`lengthRead`	read length (to check for too short fragments which can cause errors in other programs when exported)

An exported fastq file for a simulated 4C-seq sample

Carolin Walter

    if(interactive()) {
        simLibFile <- system.file("extdata", "simLib_short.csv", 
            package="Basic4CSim")
        simLib = read.csv(simLibFile, sep = "\t", header = TRUE)
        simTableFile <- system.file("extdata", "simTable_adapted.csv", 
            package="Basic4CSim")
        simTable = read.csv(simTableFile, sep = "\t", header = TRUE)
        printFastq(simTable, simLib, "test", "CATG")
    }