PLOT METHYLATION AND ANNOTATE REGION

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Description

Wrapper for plot_annotate_probes. Generates a plot of the methylation status of a region identified by DMRforPairs and associated transcripts (if annotate=TRUE).

Usage

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plot_annotate_region(tested,regions,margin=10000,regionID,clr=NA,annotate=TRUE,scores=TRUE, path)

Arguments

tested

Output of testregion

regions

Output of regionfinder

margin

See export_data

regionID

ID of a region identified by DMRforPairs as presented in the output of testregion and the output generated by export_data.

clr

See export_data

annotate

If FALSE, only basic visualizations without annotation information are generated. (default=TRUE)

scores

Specifies if statistics need to be calculated for the region or just figures. In a custom request from a user, statistics are relevant to calculate. In the export_data wrapper, they are redundant (already calculated in the testregion loop). (default=TRUE)

path

Path relative to the 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 region 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, testregion.

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

plot_annotate_region(example_output_DMRforPairs$tested,
                     example_output_DMRforPairs$regions,
                     margin=10000,
                     regionID=7,
                     annotate=FALSE,scores=TRUE,path=experiment)