Calculate the read distribution for a 4C-seq experiment

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(Basic4Cseq)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: caTools

Attaching package: 'caTools'

The following object is masked from 'package:IRanges':

    runmean

The following object is masked from 'package:S4Vectors':

    runmean

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/getReadDistribution.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getReadDistribution
> ### Title: Calculate the read distribution for a 4C-seq experiment
> ### Aliases: getReadDistribution getReadDistribution,Data4Cseq-method
> ### Keywords: getReadDistribution
> 
> ### ** Examples
> 
>   data(liverData)
>   getReadDistribution(liverData)
[1] "total reads: 2185"
[1] "reads on the viewpoint chromosome: 2185 (100% of total reads)"
[1] "reads in the viewpoint region: 1609 (73.64% of total reads)"
[1] "covered fragment ends in the viewpoint region: 62.22%"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>