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

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

Description

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.

Usage

readsToFragments(expData, fragmentLib)

Arguments

expData	Experiment data of class Data4Cseq with information on the 4C-seq experiment, including raw 4C-seq read data
fragmentLib	Fragment library for the given genome and cutting enzyme combination

Value

Data frame containing fragment-based data, i.e. a fragment's position and read coverage

Author(s)

Carolin Walter

Examples

    data(liverData)
    file <- system.file("extdata", "vfl_aagctt_catg_mm9_54_vp.csv", package="Basic4Cseq")
    rawFragments(liverData) = readsToFragments(liverData, file)
    head(rawFragments(liverData))

Basic4Cseq documentation built on Nov. 8, 2020, 6:53 p.m.