geneSetGPS {chroGPS} | R Documentation |
Given a list of genes of interest, the function highlights their position over a Multi-dimensional Scaling plot.
geneSetGPS(x, m, genes, uniqueCount = TRUE, ...)
x |
Matrix or data frame of observations x variables (tipically genes x epigenetic factors), with gene identifiers as rownames. |
m |
Object of class |
genes |
Character vector containing gene identifiers, matching those on rownames(x). |
uniqueCount |
Set to FALSE if the MDS has been generated directly from the data in
|
... |
Additional parameters given to the generic function |
Matrix with coordinates on the given input MDS object for the genes selected.
Oscar Reina
# Not run # data(s2) # d <- distGPS(s2.tab,metric='tanimoto',uniqueRows=TRUE) # mds1 <- mds(d) # set.seed(149) # sampleGenes <- rownames(s2.tab)[sample(1:nrow(s2.tab),10,rep=FALSE)] # pts <- geneSetGPS(s2.tab,mds1,genes=sampleGenes,uniqueCount=TRUE) # plot(mds1) # points(getPoints(pts),col='red',cex=3)