charm (version 2.18.0)

cmdsplot: Classical multi-dimensional scaling plot of charm data.

Description

Unsupervised clustering of charm data samples by classical multi-dimensional scaling.

Usage

cmdsplot(labcols, expcol, rawData, p, okqc=1:nrow(p), noXorY=TRUE, outfile="./cmds_topN.pdf", topN=c(100000,1000))

Arguments

labcols

vector of colors, one for each group being plotted (each unique value of pData(rawData)[,expcol])

expcol

name of the column of pData(rawData) the values of which the points are colored differently by.

rawData

the TilingFeatureSet object that p came from.

p

the matrix of percentage methylation values (scale: 0, 1) from using methp on rawData. One column per sample

okqc

vector of indices identifying which rows of p to use.

noXorY

logical value for whether or not (TRUE or FALSE) to ignore probes in chr X and Y?

outfile

file argument to pdf()

topN

Use only the

See Also

regionPlot, dmrFinder, dmrFdr

Examples

# See dmrFdr