cmdsplot {charm} | R Documentation |
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