embedPCA: Computes a PCA for a pairwise interaction matrix.

Description Usage Arguments Value Author(s) See Also Examples

View source: R/reportPCA.R

Description

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

Usage

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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

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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.