methyAnalysis (version 1.14.0)

export.methyGenoSet: 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.

Value

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

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.

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')