PLOT METHYLATION OF A CUSTOM GENOMIC REGION

Description

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

Usage

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

Arguments

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

#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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DMRforPairs)
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
Loading required package: R2HTML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DMRforPairs/plot_annotate_custom_region.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_annotate_custom_region
> ### Title: PLOT METHYLATION OF A CUSTOM GENOMIC REGION
> ### Aliases: plot_annotate_custom_region
> ### Keywords: export_visualization
> 
> ### ** Examples
> 
> #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)
$symbols_exact
[1] ""

$symbols_margin
[1] ""

$scores
                                               [,1]
beta.median.A431.beta                   0.543735652
beta.median.MCF7.beta                   0.694787330
m.median.A431.M                         0.253080817
m.median.MCF7.M                         1.186971723
median.delta.beta.A431.M.minus.MCF7.M  -0.002448525
median.delta.m.A431.M.minus.MCF7.M     -0.353212810
pairwise.p.A431.M.vs.MCF7.M                      NA
max.abs.median.delta.m                  0.353212810
p.value                                 0.845357661
n.probes                              200.000000000

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>