saveRDS-SpatialFeatureExperiment-method: Save SpatialFeatureExperiment as RDS file

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Save SpatialFeatureExperiment as RDS file

Description

Saving SFE objects as RDS files is complicated by the SpatRaster class of the images. If present, the images need to be wrapped with the wrap function in terra before serializing the SFE object. Otherwise the images will be invalid pointers when the RDS is reloaded. If the image does not fit in memory and its file source is unknown, then it will be written to a temporary file, which is reloaded when the RDS file is loaded. When an SFE object with images is read from an RDS file, the images will not be unwrapped until necessary.

Usage

## S4 method for signature 'SpatialFeatureExperiment'
saveRDS(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

Arguments

object	A SpatialFeatureExperiment object.
file	a connection or the name of the file where the R object is saved to or read from.
ascii	a logical. If TRUE or NA, an ASCII representation is written; otherwise (default), a binary one is used. See the comments in the help for save.
version	the workspace format version to use. NULL specifies the current default version (3). The only other supported value is 2, the default from R 1.4.0 to R 3.5.0.
compress	a logical specifying whether saving to a named file is to use "gzip" compression, or one of "gzip", "bzip2" or "xz" to indicate the type of compression to be used. Ignored if file is a connection.
refhook	a hook function for handling reference objects.

Value

Invisibly NULL.

Examples

outdir <- system.file("extdata", package = "SpatialFeatureExperiment")
samples <- file.path(outdir, paste0("sample0", 1:2))
sfe <- read10xVisiumSFE(samples, type = "sparse", data = "filtered")
saveRDS(sfe, "foo.rds")
# Clean up
file.remove("foo.rds")

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.