PLOT METHYLATION OF A CUSTOM GENOMIC REGION

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Description

Wrapper for plot_annotate_probes. Generates a plot of the methylation status of a custom genomic region.

Usage

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plot_annotate_custom_region(chr,st,ed,regions,margin=10000,ID="CustomRegion",clr=NA,annotate=TRUE,path)

Arguments

chr

Chromosome on which the custom region is located. Number/X/Y only (i.e. no 'chr' prefix.

st

Start position (bp) of the custom region

ed

End position (bp) of the custom region

regions

See output of regionfinder

margin

See export_data

ID

String which will be used as the file name of the figures generated. (default = "CustomRegion")

clr

See export_data

annotate

See plot_annotate_region

path

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

Details

A plot will be generated using only the probes present in the DMRforPairs output (i.e. associated to one or more of the recoded classes, see merge_classes).
Expects a writable subfolder of the curent working directory (as created by export_data()). 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 custom 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,

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"

#visualize a custom region on the genome
plot_annotate_custom_region(chr=7,
                            st=1.05E+8,
                            ed=1.06E+8,
                            example_output_DMRforPairs$regions,
                            margin=500,
                            ID="custom_region",
                            annotate=FALSE,path=experiment)