chooseNearCisFragments

chooseNearCisFragments,Data4Cseq,numeric-method

Experiment data of class <code>Data4Cseq</code> with information on the 4C-seq experiment, including fragment data for the viewpoint chromosome

expData

Interval on the viewpoint chromosome for the intended visualization

regionCoordinates

If TRUE, delete all fragments that intersect with the experiment's viewpoint interval

deleteViewpoint


    This function extracts fragment data from a <code>Data4Cseq</code> object's <code>rawFragments</code> slot for visualization with the functions <code>visualizeViewpoint</code> and <code>drawHeatmap</code> . Relevant fragments are located within the chosen visualization range; the viewpoint itself can be excluded or included.


Basic4Cseq is an R/Bioconductor package for basic
filtering, analysis and subsequent visualization of 4C-seq
data. Virtual fragment libraries can be created for any
BSGenome package, and filter functions for both reads and
fragments and basic quality controls are included. Fragment
data in the vicinity of the experiment's viewpoint can be
visualized as a coverage plot based on a running median
approach and a multi-scale contact profile.

Carolin Walter

Basic4Cseq

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

chooseNearCisFragments function

This function extracts fragment data from a <code>Data4Cseq</code> object's <code>rawFragments</code> slot for visualization with the functions <code>visualizeViewpoint</code> and <code>drawHeatmap</code> . Relevant fragments are located within the chosen visualization range; the viewpoint itself can be excluded or included.

chooseNearCisFragments: Choose fragments in a provided region around the viewpoint

Description

Usage

Arguments

Value

Examples