readsToFragments

readsToFragments,Data4Cseq,character-method

Experiment data of class <code>Data4Cseq</code> with information on the 4C-seq experiment, including raw 4C-seq read data

expData

Fragment library for the given genome and cutting enzyme combination

fragmentLib


    This function maps aligned reads to fragment ends of the virtual fragment library to calculate the coverage of the fragments. The number of reads at the start and end of a fragment is provided, as well as the average of both fragment ends.


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

readsToFragments function

This function maps aligned reads to fragment ends of the virtual fragment library to calculate the coverage of the fragments. The number of reads at the start and end of a fragment is provided, as well as the average of both fragment ends.

readsToFragments: Determine fragment coverage of a 4C-seq fragment library

Description

Usage

Arguments

Value

Examples