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Last data update: 2014.03.03

R: Computes the components of the M3D test-statistic over all...

M3D_Para

R Documentation

Computes the components of the M3D test-statistic over all regions for all sample-pairs.

Description

Parallel implementation of M3D_Wrapper function. Returns the two components of the M3D test-statistic - the MMD (Gretton et al. 2006) for the full data and the coverge only data, respectively - for all regions and all samples pairs, as a matrix.

Usage

M3D_Para(rrbs, CpGs, overlaps, num.cores = NaN)

Arguments

`rrbs`	An rrbs object containing methylation and coverage data as created using the BiSeq pacakge
`CpGs`	A GRanges object detailing the testing regions.
`overlaps`	The overlaps between the list of testing regions and the methylation data. This is obtained using the function findOverlaps(CpGs,rrbs) for a GRanges object CpGs detailing the testing regions.
`num.cores`	Integer giving the number or cores to use. Defaults to the maximum available

Value

This returns the two components of the M3D test-statistic for each region over all sample pairs as a matrix. Subtracting them gives the M3D test-statistic. This is processed with the function pvals.

Author(s)

Tom Mayo t.mayo@ed.ac.uk

References

Gretton, A., Borgwardt, K. M., Rasch, M., Scholkopf, B., Smola, A. J. (2006). A kernel method for the two-sample-problem. In Advances in neural information processing systems (pp. 513-520).

Examples

data(rrbsDemo)
data(CpGsDemo)
M3D_list <- M3D_Para(rrbsDemo,CpGsDemo)
head(M3d_list$Full-M3D_list$Coverage)

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(M3D)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/M3D/M3D_Para.Rd_%03d_medium.png", width=480, height=480)
> ### Name: M3D_Para
> ### Title: Computes the components of the M3D test-statistic over all
> ###   regions for all sample-pairs.
> ### Aliases: M3D_Para
> 
> ### ** Examples
> 
> ## No test: 
> data(rrbsDemo)
> data(CpGsDemo)
> M3D_list <- M3D_Para(rrbsDemo,CpGsDemo)
Error in M3D_Para(rrbsDemo, CpGsDemo) : 
  could not find function "detectCores"
Execution halted