M3D_Wrapper_lite: Computes the components of the M3D test-statistic over all...

In TomMayo/M3Ddevel: (development for M3D) Identifies differentially methylated regions across testing groups

Description

Returns the M3D test-statistic, without the compenents, for all regions with the cross group sample pairs averaged to save memory (in column one), as a matrix.

Usage

M3D_Wrapper_lite(rrbs, overlaps, group1 = NaN, group2 = NaN)

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.
group1	The name of the first group for the comparison. This is stored in colData(rrbs). Default finds first unique group in colData(rrbs).
group2	The name of the second group for the comparison. This is stored in colData(rrbs). Default finds second unique group in colData(rrbs).

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 [e-mail]

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)
overlaps <- findOverlaps(CpGsDemo,rrbsDemo)
M3D_list <- M3D_Wrapper_lite(rrbsDemo,overlaps)
head(M3d_list)

TomMayo/M3Ddevel documentation built on May 9, 2019, 4:53 p.m.