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 |