R: Computes the components of the M3D test-statistic over all...
M3D_Wrapper
R Documentation
Computes the components of the M3D test-statistic over all regions for all
sample-pairs.
Description
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_Wrapper(rrbs, overlaps, para = FALSE)
Arguments
rrbs
An rrbs object containing methylation and coverage data as
created using the BiSeq pacakge
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.
para
Set to true if called via M3D_Para
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.
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).
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_Wrapper.Rd_%03d_medium.png", width=480, height=480)
> ### Name: M3D_Wrapper
> ### Title: Computes the components of the M3D test-statistic over all
> ### regions for all sample-pairs.
> ### Aliases: M3D_Wrapper
>
> ### ** Examples
>
> ## No test:
> data(rrbsDemo)
> data(CpGsDemo)
> overlaps <- findOverlaps(CpGsDemo,rrbsDemo)
Error: could not find function "findOverlaps"
Execution halted