## ----echo=FALSE, results="hide", message=FALSE-------------------------------- require(knitr) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) ## ----setup, echo=FALSE, message=FALSE----------------------------------------- library(BiocSingular) set.seed(100) ## ----------------------------------------------------------------------------- dummy <- matrix(rnorm(10000), ncol=25) e.out <- runSVD(dummy, k=10, BSPARAM=ExactParam()) str(e.out) ## ----------------------------------------------------------------------------- set.seed(1000) i.out <- runSVD(dummy, k=10, BSPARAM=IrlbaParam()) ## ----------------------------------------------------------------------------- set.seed(1000) r.out <- runSVD(dummy, k=10, BSPARAM=RandomParam()) ## ----------------------------------------------------------------------------- epam <- ExactParam(fold=10) epam cr.out <- runSVD(dummy, k=10, BSPARAM=epam) ## ----------------------------------------------------------------------------- cs.out <- runSVD(dummy, k=10, scale=runif(ncol(dummy)), center=rnorm(ncol(dummy))) ## ----------------------------------------------------------------------------- set.seed(2000) def.out <- runSVD(dummy, k=10, scale=runif(ncol(dummy)), center=rnorm(ncol(dummy)), BSPARAM=IrlbaParam(deferred=TRUE)) ## ----------------------------------------------------------------------------- ipam <- IrlbaParam(tol=1e-8, extra.work=10) ipam ## ----------------------------------------------------------------------------- set.seed(3000) i.out <- runSVD(dummy, k=10, BSPARAM=ipam) ## ----------------------------------------------------------------------------- set.seed(4000) library(BiocParallel) i.out <- runSVD(dummy, k=10, BSPARAM=ipam, BPPARAM=bpparam()) ## ----------------------------------------------------------------------------- pcs.out <- runPCA(dummy, rank=10, BSPARAM=ExactParam()) str(pcs.out) ## ----------------------------------------------------------------------------- head(pcs.out$x) ## ----------------------------------------------------------------------------- sessionInfo()