embedPCA: Computes a PCA for a pairwise interaction matrix.

In RNAinteract: Estimate Pairwise Interactions from multidimensional features

Description

A principal component analysis is performed for a pairwise interaction matrix. The low-dimensional embedding is returned.

Usage

embedPCA(sgi, screen, channel,
         dim = 4, embed = "template",
         withoutgroups = c())

Arguments

sgi	An object of class RNAinteract
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.

Value

Returns a matrix with dimensions genes x dim.

Author(s)

Bernd Fischer

See Also

RNAinteract-package

Examples

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))

RNAinteract documentation built on Nov. 8, 2020, 5:28 p.m.