RNAinteract (version 1.20.0)

embedPCA: Computes a PCA for a pairwise interaction matrix.

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.

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))