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Last data update: 2014.03.03

R: Computes a PCA for a pairwise interaction matrix.

embedPCA

R Documentation

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.

Author(s)

Bernd Fischer

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))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RNAinteract)
Loading required package: abind
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAinteract/embedPCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: embedPCA
> ### Title: Computes a PCA for a pairwise interaction matrix.
> ### Aliases: embedPCA
> ### Keywords: manip
> 
> ### ** 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))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>