COMPLETE EXPORT AND VISUALIZATION OF DMRforPairs RESULTS

Description

Complete export of the DMRforPairs results. Export includes pdf's, thumbnails and TSV files describing the methylation status of all relevant (median delta M > dM_min) regions. M and beta values plotted against genomic position. Plots are generated for all samples and sample pairs (if n>2). Annotation information can be automatically looked up in the Ensembl database. If this is requested, integrated figures of the methylation pattern are generated including all transcripts annotated to the region of interest (+margin). This function also generates overviews (tables) in tsv and HTML format with information about the regions and their methylation status in the samples. This is done separately for all regions, regions with a relevant difference and regions with a significant difference.

Usage

export_data (tested,regions,th=0.05,annotate.relevant=FALSE,annotate.significant=TRUE,FigsNotRelevant=FALSE, min_n=4,min_dM=1.4,min_distance=200,margin=10000,clr=NA,method="fdr", experiment.name,debug=FALSE)

Arguments

Details

In the output is organized according to all, relevant and significant regions:

1. all: all regions identified by DMRforPairs

2. relevant: regions identified by DMRforPairs with a median difference in M values between any pair of samples of > min_dM

3. significant: relevant + Kruskall Wallis test shows a significant result (<th)

Writing permissions are required in the working directory when using the export and visualization functions of DMRforPairs. Internet access is required to use the annotation features.
By default, DMRforPairs creates a folder (experiment.name) within the current working directory in which the output is stored. This is done within the export_data wrapper which should be run before any other (specific) analysis are performed (exploration phase, see DMRforPairs-package. A complete export generates a large number of files which are stored out of sight (experiment.name/figures). Figures and overviews of statistics are most conveniently accessed through the HTML tables.

Value

The output is comparable to that of testregion, supplemented with external links (Ensembl, UCSC) and annotation info if requested.

Author(s)

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

See Also

DMRforPairs, regionfinder, testregion, plot_annotate_region, plot_annotate_probes.

Examples

#For the this step, pleas 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.
data(DMRforPairs_data)
experiment="example_DMRforPairs"

#Export the results from output using the default settings;
#annotation is disabled as to prevent problems on (build)
#systems without an internet connection. A folder 
#"example_DMRforPairs" containing the resuls is created in 
#your working directory.
tested_inclannot=export_data(tested=example_output_DMRforPairs$tested, 
regions=example_output_DMRforPairs$regions, 
experiment.name=experiment,
annotate.significant=FALSE,
annotate.relevant=FALSE)

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/export_data.Rd_%03d_medium.png", width=480, height=480)
> ### Name: export_data
> ### Title: COMPLETE EXPORT AND VISUALIZATION OF DMRforPairs RESULTS
> ### Aliases: export_data
> ### Keywords: export_visualization
> 
> ### ** Examples
> 
> #For the this step, pleas 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.
> data(DMRforPairs_data)
> experiment="example_DMRforPairs"
> 
> #Export the results from output using the default settings;
> #annotation is disabled as to prevent problems on (build)
> #systems without an internet connection. A folder 
> #"example_DMRforPairs" containing the resuls is created in 
> #your working directory.
> tested_inclannot=export_data(tested=example_output_DMRforPairs$tested, 
+ regions=example_output_DMRforPairs$regions, 
+ experiment.name=experiment,
+ annotate.significant=FALSE,
+ annotate.relevant=FALSE)
Preparing export
Generating images for relevant regions (if annotation is requested, this can take quite long).
Generating images for significant regions (if annotation is requested, this can take quite long).
Exporting tables (HTML & CSV)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>