as.loom: Convert objects to loom objects

Description Usage Arguments Details See Also Examples

View source: R/generics.R

Description

Convert objects to loom objects

Usage

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as.loom(x, ...)

## S3 method for class 'Seurat'
as.loom(
  x,
  assay = NULL,
  filename = file.path(getwd(), paste0(Project(object = x), ".loom")),
  max.size = "400mb",
  chunk.dims = NULL,
  chunk.size = NULL,
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

x

An object to convert to class loom

...

Ignored for now

assay

Assay to store in loom file

filename

The name of the new loom file

max.size

Set maximum chunk size in terms of memory usage, unused if chunk.dims is set; may pass a character string (eg. 3gb, 1200mb) or exact value in bytes

chunk.dims

Matrix chunk dimensions; auto-determined by default

chunk.size

Maximum number of cells read/written to disk at once; auto-determined by default

overwrite

Overwrite an already existing loom file?

verbose

Display a progress bar

Details

The Seurat method for as.loom will try to automatically fill in datasets based on data presence. For example, if an assay's scaled data slot isn't filled, then dimensional reduction and graph information will not be filled, since those depend on scaled data. The following is a list of how datasets will be filled

See Also

create

Examples

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## Not run: 
lfile <- as.loom(x = pbmc_small)

## End(Not run)

Seurat documentation built on Jan. 13, 2021, 7:11 p.m.