Package: randPedPCA 1.1.3

randPedPCA: Fast PCA for Large Pedigrees

Carry out principal component analysis (PCA) of very large pedigrees such as found in breeding populations! This package exploits sparse matrices and randomised linear algebra to deliver a gazillion-times speed-up compared to naive singular value decoposition (SVD) (and eigen decomposition).

Authors:Hanbin Lee [aut], Hannes Becher [cre], Ros Craddock [aut], Gregor Gorjanc [aut]

randPedPCA_1.1.3.tar.gz
randPedPCA_1.1.3.zip(r-4.7-any)randPedPCA_1.1.3.zip(r-4.6-any)randPedPCA_1.1.3.zip(r-4.5-any)
randPedPCA_1.1.3.tgz(r-4.6-any)randPedPCA_1.1.3.tgz(r-4.5-any)
randPedPCA_1.1.3.tar.gz(r-4.7-any)randPedPCA_1.1.3.tar.gz(r-4.6-any)
randPedPCA_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
randPedPCA/json (API)

# Install 'randPedPCA' in R:

install.packages('randPedPCA', repos = c('https://bryo-han.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

pedLInv - L inverse matrix of the one-population example pedigree
pedLInv2 - L inverse matrix of the two-population example pedigree
pedLInv4 - L inverse matrix of the four-population example pedigree
pedMeta - Metadata associated with one-population example
pedMeta2 - Metadata associated with the two-population example pedigree
pedMeta4 - Metadata associated with the four-population example pedigree

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 9 scripts 276 downloads 9 exports 8 dependencies

Last updated from:5ee6c8864e. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	123
source / vignettes	OK	449
linux-release	OK	281
macos-release	OK	134
macos-oldrel	OK	204
windows-devel	OK	112
windows-release	OK	341
windows-oldrel	OK	81
wasm-release	OK	220

Exports:dspc hutchpp importLinv plot3D plot3DWithProj randRangeFinder randSVD rppca sparse2spam

Dependencies:dotCall64 lattice Matrix pedigreeTools Rcpp RcppEigen RSpectra spam

Pedigree PCA

Intro | Pedigree input | Matrix input | Centring | Variance components | Estimating the total variance from an $L^{-1}$ matrix | Variance components - Examples | Plotting | Down-sampling | Performance | Using one's own data

Rendered frompedigree-pca.Rmdusingknitr::rmarkdown

Last update: 2025-06-16
Started: 2025-04-24

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Readme and manuals

Help Manual

Help page	Topics
Add downsampling index to rppca object	dspc
Compute the number of vectors to use for Hutchinson trace estimation	getNumVectorsHutchinson
Hutch++ trace estimation	hutchpp
Generate spam object from L inverse file	importLinv
L inverse matrix of the one-population example pedigree	pedLInv
L inverse matrix of the two-population example pedigree	pedLInv2
L inverse matrix of the four-population example pedigree	pedLInv4
Metadata associated with one-population example	pedMeta
Metadata associated with the two-population example pedigree	pedMeta2
Metadata associated with the four-population example pedigree	pedMeta4
3D plot using rgl	plot3D
3D plot of PC scores with projections on coordinate planes	plot3DWithProj
Generate range matrix for SVD	randRangeFinder
Singular value decomposition in sparse triangular matrix	randSVD
Trace estimation for sparse L inverse matrices	randTraceHutchinson
Fast pedigree PCA using sparse matrices and randomised linear algebra	rppca rppca.pedigree rppca.spam
Convert generic sparse matrix to spam format	sparse2spam

Package: randPedPCA 1.1.3

randPedPCA: Fast PCA for Large Pedigrees

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)