R Graphical Manual

Last data update: 2014.03.03

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

cmdsplot

R Documentation

Classical multi-dimensional scaling plot of charm data.

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

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

`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

Martin Aryee <aryee@jhu.edu>, Peter Murakami, Rafael Irizarry

# See dmrFdr