PLOT METHYLATION VALUES AROUND A GENE

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Description

Wrapper for plot_annotate_probes. Generates a plot of the methylation status of / around a specific gene.

Usage

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plot_annotate_gene(gs,regions,margin=10000,ID,clr=NA,annotate=TRUE,path)

Arguments

gs

Gene Symbol of interest

regions

Output of regionfinder

margin

See export_data

ID

Custom string which will be used as the file name of the figures generated

clr

See export_data

annotate

See plot_annotate_region

path

Path relative to the current working directory to save the files (=experiment.name in export_data)

Details

Expects a subfolder with the name of your experiment to exist as created by export_data(). Writing permissions are required in the working directory to use the export and visualization functions of DMRforPairs. Internet access is required to use the annotation features.

Value

A number of figures (including pairwise plots if n>2) is generated visualizing methylation status in the samples at / near the gene investigated. Statistics and optional annotation information are reported back by the function.

Author(s)

Martin Rijlaarsdam, m.a.rijlaarsdam@gmail.com

See Also

export_data, plot_annotate_probes, regionfinder,

Examples

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#For the this step, please ensure that you have writing 
#permissions in your working directory. If any of the
#annotate parameters is set to TRUE, an internet connection
#is required.

#This example expects a folder "example_DMRforPairs" to exist and
#be writable in the current working directory.
data(DMRforPairs_data)
experiment="example_DMRforPairs"

plot_annotate_gene(gs="DUS4L",
                   regions=example_output_DMRforPairs$regions,
                   margin=10000,
                   ID="DUS4L",
                   annotate=FALSE,path=experiment)