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

In charm: Analysis of DNA methylation data from CHARM microarrays

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

Author(s)

Martin Aryee <[e-mail]>, Peter Murakami, Rafael Irizarry

See Also

regionPlot, dmrFinder, dmrFdr

Examples

# See dmrFdr

charm documentation built on May 6, 2019, 2:29 a.m.