saveDataset: Save a dataset to disk
In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

saveDataset

R Documentation

Save a dataset to disk

Description

Save a single-cell dataset to disk, usually in preparation for upload.

Usage

saveDataset(x, path, metadata)

Arguments

`x`	A SummarizedExperiment or one of its subclasses.
`path`	String containing the path to a new directory in which to save `x`. Any existing directory is removed before saving `x`.
`metadata`	Named list containing metadata for this dataset, see the schema returned by `fetchMetadataSchema()`. Note that the `applications.takane` property will be automatically added by this function and does not have to be supplied.

Value

x and its metadata are saved into path, and NULL is invisibly returned.

Author(s)

Aaron Lun

Examples

library(SingleCellExperiment)
sce <- SingleCellExperiment(list(counts=matrix(rpois(1000, lambda=1), 100, 10)))
rownames(sce) <- sprintf("GENE_%i", seq_len(nrow(sce)))
colnames(sce) <- head(LETTERS, 10)

meta <- list(
    title="My dataset",
    description="This is my dataset",
    taxonomy_id="10090",
    genome="GRCh38",
    sources=list(list(provider="GEO", id="GSE12345")),
    maintainer_name="Shizuka Mogami",
    maintainer_email="mogami.shizuka@765pro.com"
)

tmp <- tempfile()
saveDataset(sce, tmp, meta)
list.files(tmp, recursive=TRUE)
alabaster.base::readObject(tmp)

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.