embedPCA {RNAinteract} | R Documentation |
A principal component analysis is performed for a pairwise interaction matrix. The low-dimensional embedding is returned.
embedPCA(sgi, screen, channel, dim = 4, embed = "template", withoutgroups = c())
sgi |
An object of class |
screen |
The screen name whose interaction matrix will be embedded. |
channel |
The channel name whose interaction matrix will be embedded. |
dim |
The embedding dimension. |
embed |
Either "template" (default) or "query" denotes if the embedding is done for rows or columns. |
withoutgroups |
Genes annotated with these groupnames are not considered for embedding. |
Returns a matrix with dimensions genes x dim.
Bernd Fischer
data("sgi") X <- embedPCA(sgi, screen="1", channel="nrCells", dim=2) plot(X[,1], X[,2], pch=20, cex=0.01) text(X[,1], X[,2], row.names(X))