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

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

Description

This function provides some 4C-seq quality statistics based on the experiment's read distribution throughout the genome. getReadDistribution 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.

Usage

getReadDistribution(expData, distanceFromVP = 100000, useFragEnds = TRUE, outputName = "")

Arguments

expData	Experiment data of class Data4Cseq with information on the 4C-seq experiment
distanceFromVP	Distance from the viewpoint that is checked for covered fragments
useFragEnds	If TRUE, the function uses fragment end data; if FALSE, an average value for whole fragments is used.
outputName	An optional name for an output text file containing the statistics data

Value

Text with statistics data on the 4C-seq experiment

Note

Text export is supported; if no file name is provided, the results are printed on screen.

Author(s)

Carolin Walter

References

van de Werken, H., de Vree, P., Splinter, E., et al. (2012): 4C technology: protocols and data analysis, Methods Enzymology, 513, 89-112

Examples

    data(liverData)
    getReadDistribution(liverData)

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