methyl_MDS_plot {DAMEfinder} | R Documentation

## 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)

[Package DAMEfinder version 1.6.0 Index]