export-method: Export LoomExperiment to LoomFile

In Bioconductor/LoomExperiment: LoomExperiment container

Export LoomExperiment to LoomFile

Description

Exports a LoomExperiment to a LoomFile. Note the colGraph and rowGraph contained within the LoomExperimnet object are 1-indexed in R and are converted to 0-indexed in the loom file.

Usage

## S4 method for signature 'LoomExperiment,LoomFile,ANY'
export(object, con,
    matrix=assayNames(object)[1], rownames_attr="rownames", colnames_attr="colnames")

Arguments

object	A LoomExperiment object to be exported. File must have the .loom extension.
con	The connection from which data is loaded or to which data is saved. If this is a character vector, it is assumed to be a filename and a corresponding file connection is created and then closed after exporting the object. If a RTLFile derivative, the data is loaded from or saved to the underlying resource.
matrix	A matrix in which the column and rows for the Loom file will be derived. The default argument is dervied from the the first assay in the LoomExperiment object.
rownames_attr	A character vector indicating the name of the rowData attribute to represent the names rownames in the LoomExperiment object.
colnames_attr	A character vector indicating the name of the colData attribute to represent the names colnames in the LoomExperiment object.

Value

An error code indiciating whether the operation was successful.

See Also

LoomExperiment, LoomFile,

Examples

counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
sce <- SingleCellExperiment(assays = list(counts = counts))
scle <- SingleCellLoomExperiment(sce)
tempfile <- tempfile(fileext=".loom")
export(scle, tempfile)

Bioconductor/LoomExperiment documentation built on Nov. 2, 2024, 9:57 p.m.