Scale4C: Creating a Scale4C object

In Scale4C: Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

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

Scale4C documentation built on Nov. 8, 2020, 8:21 p.m.