Fast PCA for Large Pedigrees


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Documentation for package ‘randPedPCA’ version 1.0.1

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dspc Add downsampling index to rppca object
getNumVectorsHutchinson Compute the number of vectors to use for Hutchinson trace estimation
hutchpp Hutch++ trace estimation
importLinv Generate spam object from L inverse file
pedLInv Example pedigree L inverse matrix
pedLInv2 Example pedigree L inverse matrix
pedLInv4 Example pedigree L inverse matrix
pedMeta Metadata associated with the example pedigree
pedMeta2 #' Example genotype data #' #' An genotype matrix (0/1/2) generated from an AlphaSimR simulation of 20 generations. #' An original population splits into sub-populations A and B. After a number of #' generations, crossbreeding starts. #' #' #' @format ## 'pedGeno' #' Matrix of 2650 rows (inidividuals) and 11000 columns (SNPs) #' @source Simulation "pedGeno" Metadata associated with the 2nd example pedigree
pedMeta4 #' Example genotype data 2 #' #' An genotype matrix (0/1/2) generated from an AlphaSimR simulation of 20 generations. #' Two diverged populations A and B. After a number of #' generations, crossbreeding starts. #' #' #' @format ## 'pedGeno2' #' Matrix of 2650 rows (inidividuals) and 11000 columns (SNPs) #' @source Simulation "pedGeno2" Metadata associated with the 2nd example pedigree
plot3D 3D plot using rgl
plot3DWithProj 3D plot of PC scores with projections on coordinate planes
randRangeFinder Generate range matrix for SVD
randSVD Singular value decomposition in sparse triangular matrix
randTraceHutchinson Trace estimation for sparse L inverse matrices
rppca Fast pedigree PCA using sparse matrices and randomised linear algebra
rppca.pedigree Fast pedigree PCA using sparse matrices and randomised linear algebra
rppca.spam Fast pedigree PCA using sparse matrices and randomised linear algebra
sparse2spam Convert generic sparse matrix to spam format