PUMA Principal Components Analysis

Description

This function carries out principal components analysis (PCA), taking into account not only the expression levels of genes, but also the variability in these expression levels.

The various other pumaPCA... functions are called during the execution of pumaPCA

Usage

pumaPCA(
    eset
,   latentDim           = 	if(dim(exprs(eset))[2] <= 3)
 								dim(exprs(eset))[[2]]-1
							else
								3
,   sampleSize          =	if(dim(exprs(eset))[1] <= 1000)
								 dim(exprs(eset))[[1]]
							else
								1000	## Set to integer or FALSE for all
,   initPCA             =	TRUE	## Initialise parameters with PCA
,   randomOrder         =	FALSE	## Update parameters in random order
,   optimMethod         =	"BFGS"  ## ?optim for details of methods
,   stoppingCriterion   =	"deltaW"## can also be "deltaL"
,   tol                 =	1e-3	## Stop when delta update < this
,   stepChecks          =	FALSE	## Check likelihood after each update?
,   iterationNumbers    =	TRUE	## Show iteration numbers?
,   showUpdates         =	FALSE	## Show values after each update?
,   showTimings         =	FALSE	## Show timings after each update?
,   showPlot            =	FALSE	## Show projection plot after each update?
,   maxIters            =	500		## Number of EM iterations.
,   transposeData       =	FALSE	## Transpose eset matrices?
,   returnExpectations  =	FALSE
,   returnData          =	FALSE
,   returnFeedback      =	FALSE
,	pumaNormalize		=	TRUE
)

Arguments

Value

An object of class pumaPCARes

Author(s)

Richard D. Pearson

See Also

Related methods pumaDE, createDesignMatrix and createContrastMatrix

Examples

	#	Next 4 lines commented out to save time in package checks, and saved version used
    # if (require(affydata)) {
	#	data(Dilution)
	#	eset_mmgmos <- mmgmos(Dilution)
	# }
	data(eset_mmgmos)

	pumapca_mmgmos <- pumaPCA(eset_mmgmos)
	plot(pumapca_mmgmos)

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(puma)
Loading required package: oligo
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

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/puma/pumaPCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pumaPCA
> ### Title: PUMA Principal Components Analysis
> ### Aliases: pumaPCA pumaPCAEstep pumaPCALikelihoodBound
> ###   pumaPCALikelihoodCheck pumaPCANewtonUpdateLogSigma newtonStep
> ###   pumaPCARemoveRedundancy pumaPCASigmaGradient pumaPCASigmaObjective
> ###   pumaPCAUpdateCinv pumaPCAUpdateM pumaPCAUpdateMu pumaPCAUpdateW
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 	#	Next 4 lines commented out to save time in package checks, and saved version used
>     # if (require(affydata)) {
> 	#	data(Dilution)
> 	#	eset_mmgmos <- mmgmos(Dilution)
> 	# }
> 	data(eset_mmgmos)
> 
> 	pumapca_mmgmos <- pumaPCA(eset_mmgmos)
Iteration number: 1
Iteration number: 2
Iteration number: 3
Iteration number: 4
> 	plot(pumapca_mmgmos)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>