M3D_Wrapper_lite {M3D} | R Documentation |
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.
M3D_Wrapper_lite(rrbs, overlaps, group1 = NaN, group2 = NaN, verbose = TRUE)
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). |
verbose |
Logical vector. If true, the function prints a progress bar. |
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.
Tom Mayo t.mayo@ed.ac.uk
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).
data(rrbsDemo) data(CpGsDemo) CpGsDemo <- CpGsDemo[1:5] overlaps <- GenomicRanges::findOverlaps(CpGsDemo,rrbsDemo) M3D_list <- M3D_Wrapper_lite(rrbsDemo,overlaps) head(M3D_list)