Data4Cseq: Creating a Data4Cseq object

Description

This function creates a Data4Cseq object. Data on the 4C-seq experiment, e.g. the chromosome of the viewpoint, is stored and checked for consistency.

Usage

Data4Cseq(viewpointChromosome, viewpointInterval, readLength, pointsOfInterest, rawReads)

Arguments

viewpointChromosome

The experiment's viewpoint chromosome

viewpointInterval

The interval of the experiment's viewpoint, consisting of a start and end coordinate

readLength

The experiment's read length (in base pairs)

pointsOfInterest

Points of interest to be marked in a near-cis visualization

rawReads

Reads of the 4C-seq experiment, aligned and stored as an GAlignments object

Value

An instance of the Data4Cseq class.

Details

A Data4Cseq object contains basic information for the corresponding 4C-seq experiment, including the viewpoint chromosome, the viewpoint region and reads from the experiment. See Data4Cseq-class for more details. The constructor collects the basic data; fragment data or normalized read counts are added later.

Fragments at the experiment's viewpoint are usually vastly overrepresented due to self-ligation; chooseNearCisFragments offers the option to discard all fragments in the specified viewpoint region. The specified viewpoint interval of a Data4Cseq object is supposed to correspond to the positions of the biological primers on the genome, but can also be increased in size if more fragments around the viewpoint should be removed.

Examples

Run this code

  # create a Data4Cseq object with a minimum of data
  liverData = Data4Cseq(viewpointChromosome = "10", viewpointInterval = c(20879870, 20882209), readLength = 54)
  liverData

  # create a Data4Cseq object, including possible points of interest and raw reads 
  bamFile <- system.file("extdata", "fetalLiverShort.bam", package="Basic4Cseq")
  liverReads <- readGAlignments(bamFile)
  pointsOfInterestFile <- system.file("extdata", "fetalLiverVP.bed", package="Basic4Cseq")
  liverData = Data4Cseq(viewpointChromosome = "10", viewpointInterval = c(20879870, 20882209), readLength = 54, pointsOfInterest = readPointsOfInterestFile(pointsOfInterestFile), rawReads = liverReads)
  liverData