export.methyGenoSet {methyAnalysis} | R Documentation

## Export a MethyGenoSet object to be visualized using external genome browser tools

### Description

Export a MethyGenoSet object to be visualized in IGV, IGB or other tools. Current version supports "gct" or "bw" formats.

### Usage

    export.methyGenoSet(methyGenoSet, file.format = c("gct", "bw"), exportValue = c("beta", "M", "intensity"), hgVersion.default = "hg19", savePrefix = NULL, outputFile=NULL)

### Arguments

`methyGenoSet` | A MethyGenoSet object.
`file.format` | Export file format
`exportValue` | Export methylation values
`hgVersion.default` | The default human genome version
`savePrefix` | The prefix used in the output filename. Only valid when outputFile is NULL.
`outputFile` | The output file name provided by the user. If file.format is "bw", outputFile should be a character vector with the same length as the sample number, or else it will be ignored.

### Details

An easy way to visualize DNA methylation data is to export the DNA methylation data in certain formats, and visualize these files using some external genome browser tools, like IGV (http://www.broadinstitute.org/igv/) and IGB (http://bioviz.org/igb/index.html). The current implementation of this function supports two output formats: ".gct" and ".bw" files. ".gct" includes all samples in a single file. It is only supported by IGV genome browser. The BigWig format (".bw") is a more general format supported by many visualization tools. Each BigWig file represents one single sample. So it is more flexible for the users only interested in a subset of samples.

### Value

Output "gct" (for IGV) or "bw" (BigWig) files

### Author(s)

Pan Du

### References

IGV: http://www.broadinstitute.org/igv/ IGB: http://bioviz.org/igb/index.html

### Examples

    	data(exampleMethyGenoSet)
    	export.methyGenoSet(exampleMethyGenoSet, file.format='gct', savePrefix='test')
    	# export.methyGenoSet(exampleMethyGenoSet, file.format='bw', savePrefix='test')

[Package methyAnalysis version 1.31.0 Index]