bigpca: PCA, Transpose and Multicore Functionality for 'big.matrix' Objects

Adds wrappers to add functionality for big.matrix objects (see the bigmemory project). This allows fast scalable principle components analysis (PCA), or singular value decomposition (SVD). There are also functions for transposing, using multicore 'apply' functionality, data importing and for compact display of big.matrix objects. Most functions also work for standard matrices if RAM is sufficient.

Author
Nicholas Cooper
Date of publication
2015-11-08 08:40:28
Maintainer
Nicholas Cooper <nick.cooper@cimr.cam.ac.uk>
License
GPL (>= 2)
Version
1.0.3

View on CRAN

Man pages

big.algebra.install.help
Attempt to install the bigalgebra package
big.PCA
PCA/Singular Value Decomposition for big.matrix
bigpca-internal
Internal bigpca Functions
bigpca-package
PCA, Transpose and Multicore Functionality for 'big.matrix'...
big.select
Select a subset of a big.matrix
big.t
Transpose function for big.matrix objects
bmcapply
A multicore 'apply' function for big.matrix objects
estimate.eig.vpcs
Estimate the variance percentages for uncalculated...
generate.test.matrix
Generate a test matrix of random data
get.big.matrix
Retrieve a big.matrix object
import.big.data
Load a text file into a big.matrix object
pca.scree.plot
Make scree plots for any PCA
PC.correct
Correct a big.matrix by principle components
prv.big.matrix
Tidier display function for big matrix objects
quick.elbow
Quickly estimate the 'elbow' of a scree plot (PCA)
quick.pheno.assocs
Quick association tests for phenotype
select.least.assoc
Select subset of rows least associated with a categorical...
subcor.select
Selection of the most correlated variable subset
subpc.select
Selection of a representative variable subset
svn.bigalgebra.install
Attempt to install the bigalgebra package using SVN
thin
Reduce one dimension of a large matrix in a strategic way
uniform.select
Derive a subset of a large dataset

Files in this package

bigpca
bigpca/NAMESPACE
bigpca/R
bigpca/R/bigpca.R
bigpca/MD5
bigpca/DESCRIPTION
bigpca/man
bigpca/man/big.t.Rd
bigpca/man/prv.big.matrix.Rd
bigpca/man/select.least.assoc.Rd
bigpca/man/quick.pheno.assocs.Rd
bigpca/man/svn.bigalgebra.install.Rd
bigpca/man/estimate.eig.vpcs.Rd
bigpca/man/subpc.select.Rd
bigpca/man/bigpca-package.Rd
bigpca/man/big.select.Rd
bigpca/man/import.big.data.Rd
bigpca/man/pca.scree.plot.Rd
bigpca/man/bigpca-internal.Rd
bigpca/man/quick.elbow.Rd
bigpca/man/big.algebra.install.help.Rd
bigpca/man/big.PCA.Rd
bigpca/man/PC.correct.Rd
bigpca/man/uniform.select.Rd
bigpca/man/subcor.select.Rd
bigpca/man/thin.Rd
bigpca/man/get.big.matrix.Rd
bigpca/man/bmcapply.Rd
bigpca/man/generate.test.matrix.Rd