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randPedPCA (version 1.1.3)

Fast PCA for Large Pedigrees

Description

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).

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Version

Install

install.packages('randPedPCA')

Monthly Downloads

248

Version

1.1.3

License

GPL (>= 2)

Maintainer

Hannes Becher

Last Published

July 22nd, 2025

Functions in randPedPCA (1.1.3)

Hutch++ trace estimation

L inverse matrix of the one-population example pedigree

Add downsampling index to rppca object

getNumVectorsHutchinson

Compute the number of vectors to use for Hutchinson trace estimation

Convert generic sparse matrix to spam format

randRangeFinder

Generate range matrix for SVD

Generate spam object from L inverse file

Singular value decomposition in sparse triangular matrix

L inverse matrix of the four-population example pedigree

Metadata associated with the two-population example pedigree

L inverse matrix of the two-population example pedigree

Metadata associated with one-population example

3D plot using rgl

3D plot of PC scores with projections on coordinate planes

Metadata associated with the four-population example pedigree

Fast pedigree PCA using sparse matrices and randomised linear algebra

randTraceHutchinson

Trace estimation for sparse L inverse matrices