grab scvi-tools VAE instance built on the PBMC datasets following the tutorial

Source: R/cache_citeseq_pbmcs.R

grab scvi-tools VAE instance built on the PBMC datasets following the tutorial

cacheCiteseq5k10kTutvae()

Value

invisibly, the path to the .zip file holding the fitted VAE and associated data

Note

VAE construction followed tutorial at `https://docs.scvi-tools.org/en/stable/tutorials/notebooks/totalVI.html`.

It may be advantageous to set `options(timeout=3600)` or to allow an even greater time for internet downloads, if working at a relatively slow network connection.

Examples

zpath <- cacheCiteseq5k10kTutvae()
td <- tempdir()
utils::unzip(zpath, exdir = td)
vaedir <- paste0(td, "/vae2_ov")
scvi <- scviR()
adm <- anndataR()
hpath <- cacheCiteseq5k10kPbmcs()
adata <- adm$read(hpath)
mod <- scvi$model$`_totalvi`$TOTALVI$load(vaedir, adata, use_gpu = FALSE)
mod
#>