getReadDistribution

getReadDistribution,Data4Cseq-method

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

expData

Distance from the viewpoint that is checked for covered fragments

distanceFromVP

If TRUE, the function uses fragment end data; if FALSE, an average value for whole fragments is used.

useFragEnds

An optional name for an output text file containing the statistics data

outputName


This function provides some 4C-seq quality statistics based on the experiment's read distribution throughout the genome. <code>getReadDistribution</code> calculates the number of total reads, cis to overall ratio of reads, and the percentage of covered fragment ends within a certain distance around the experiment's viewpoint. Reference values for high-quality experiments, as provided by van de Werken et al, 2012, are more than one million reads total, a cis to overall ratio of more than 40% and a large fraction of covered fragment ends in the viewpoint's vicinity. 


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

getReadDistribution function

This function provides some 4C-seq quality statistics based on the experiment's read distribution throughout the genome. <code>getReadDistribution</code> calculates the number of total reads, cis to overall ratio of reads, and the percentage of covered fragment ends within a certain distance around the experiment's viewpoint. Reference values for high-quality experiments, as provided by van de Werken et al, 2012, are more than one million reads total, a cis to overall ratio of more than 40% and a large fraction of covered fragment ends in the viewpoint's vicinity.

getReadDistribution: Calculate the read distribution for a 4C-seq experiment

Description

Usage

Arguments

Value

References

Examples