| 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 |