rebuildIndex: Rebuild the index

In LTLA/SingleR: Reference-Based Single-Cell RNA-Seq Annotation

Rebuild the index

Description

Rebuild the index (or indices), typically after restarting the R session. This is because the indices are held in external memory and are not serialized correctly by R.

Usage

rebuildIndex(trained, num.threads = 1)

Arguments

trained	List containing the output of trainSingleR, possibly after some operations that invalidate the indices.
num.threads	Integer specifying the number of threads to use for training.

Value

trained is returned with valid indices. If it already had valid indices, this function is a no-op.

Author(s)

Aaron Lun

Examples

# Making up the training set.
ref <- .mockRefData()
ref <- scuttle::logNormCounts(ref)
trained <- trainSingleR(ref, ref$label)
trained$built # a valid address

# Saving and reloading the index.
tmp <- tempfile(fileext=".rds")
saveRDS(trained, file=tmp)
reloaded <- readRDS(tmp)
reloaded$built # not valid anymore

rebuilt <- rebuildIndex(reloaded)
rebuilt$built # back to validity

LTLA/SingleR documentation built on Feb. 28, 2024, 2:05 a.m.