Scale4C {Scale4C} | R Documentation

## Creating a Scale4C object

### Description

This function creates a Scale4C object. Data on the 4C-seq experiment, i.e. read counts per fragment and viewpoint coordinates, are stored and checked for plausibility.

### Usage

    Scale4C(viewpoint, viewpointChromosome, rawData)

### Arguments

`viewpoint` | The experiment's viewpoint (start, single coordinate)
`viewpointChromosome` | The experiment's viewpoint Chromosome
`rawData` | Reads of the 4C-seq experiment per fragment on an interval of interest (GRanges object with position and read data)

### Details

A `Scale4C` object contains the basic information on a 4C-seq experiment for a certain interval of interest, i.e. read counts at given positions. See `Scale4C-class` for details. Scale-space features such as fingerprint maps or tesselation are calculated during further steps of the analysis by the appropriate functions.

Scale4C expects the raw data to be in a simple data frame consisting of 'position' and 'reads'. `importBasic4CseqData` allows to import fragment data from Basic4Cseq for convenience, however, preparing and importing a simple table with two columns into R is sufficient.

### Value

An instance of the Scale4C class.

### Author(s)

Carolin Walter

### See Also

`Scale4C-class`

### Examples

        # create a Scale4C object from a Basic4Cseq export table with added
        # viewpoint data
        csvFile <- system.file("extdata", "liverData.csv", package="Scale4C")
        liverReads <- importBasic4CseqData(csvFile, viewpoint = 21160072,
            viewpointChromosome = "chr10", distance = 1000000)
        liverData = Scale4C(rawData = liverReads, viewpoint = 21160072,
            viewpointChromosome = "chr10")
        liverData

[Package Scale4C version 1.2.0 Index]