Description Usage Arguments Value Author(s) Examples
Given a list of genes of interest, the function highlights their position over a Multi-dimensional Scaling plot.
1 | 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
1 2 3 4 5 6 7 8 9 | # 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)
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