printWigFile: Print a wig file from 4C-seq read data

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

Description

This function provides wig files from filtered fragment data. Only reads on unique frag-ends are considered for the export. Export of wig files with a fixed span length requires a uniform read length throughout the data.

While some tools (e.g. the Integrative Genomics Viewer, IGV) accept 'raw' wig data, the UCSC browser needs a header line for correct visualizations. A basic header line has the form 'track type=wiggle_0', but may also contain information on the track's name and a short description. Since the header line may complicate possible downstream analysis of the wig files, no header is included per default.

Usage

printWigFile(expData, wigFileName = "output.wig", fixedSpan = TRUE, headerUCSC = "", useOnlyIndex = FALSE)

Arguments

expData	Experiment data of class Data4Cseq with information on the 4C-seq experiment
wigFileName	Name of the wig file that is written to hard disk
fixedSpan	If TRUE, use a fixed span for the wig file
headerUCSC	A header line for the UCSC browser
useOnlyIndex	If TRUE, use only '1,2,...Y' as chromosome names, if FALSE, use 'chr1,chr2...chrY'.

Value

A wig file containing the experiment's reads

Author(s)

Carolin Walter

References

UCSC Genome Browser: Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.

http://genome.ucsc.edu/

Examples

    if(interactive()) {
        data(liverData)
        printWigFile(liverData, wigFileName = "fetalLiver.wig")
    }

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