methyl_MDS_plot: Multidimensional scaling plot of distances between...

In markrobinsonuzh/DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

Multidimensional scaling plot of distances between methylation proportions (beta values)

Description

Same as plotMDS, except for an arc-sine transformation of the methylation proportions.

Usage

methyl_MDS_plot(x, group, top = 1000, coverage = 5, adj = 0.02, pointSize = 4)

Arguments

x	RangedSummarizedExperiment, output from calc_derivedasm or calc_asm.
group	Vector of group or any other labels, same length as number of samples.
top	Number of top CpG sites used to calculate pairwise distances.
coverage	Minimum number of reads covering a CpG site on each allele. Default = 5.
adj	Text adjustment in y-axis. Default = 0.2.
pointSize	Default = 4.

Value

Two-dimensional MDS plot.

Examples

data(readtuples_output)
ASM <- calc_asm(readtuples_output)
grp <- factor(c(rep('CRC',3),rep('NORM',2)), levels = c('NORM', 'CRC'))
methyl_MDS_plot(ASM, grp)

markrobinsonuzh/DAMEfinder documentation built on April 7, 2023, 6:37 a.m.