saveATAC: A function to save a scATAC-seq dataset stored in a...

In shooshtarilab/scATAC.Explorer: A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata

A function to save a scATAC-seq dataset stored in a SingleCellExperiment

Description

This function allows you to save the counts, peaks, cell ID's/barcodes, and any cell clustering data to disk in csv format. It takes two options: an object to save and a directory to save in. Multiple files will be created in the provided output directory, one for each type of data available in the scATAC_data object (counts, cell ID/Barcode, peak regions, cell type/cluster annotations).

Usage

saveATAC(object, outdir)

Arguments

object	The SingleCellExperiment object to be written to disk, this should be an individual dataset returned by queryATAC.
outdir	The directory to save the data in, the directory should not exist yet.

Value

Nothing

Examples

# Retrieve a previously identified dataset (see queryATAC) and save it to disk
res <- queryATAC(accession = 'GSE89362')[[1]]

saveATAC(res, output_directory_name)

shooshtarilab/scATAC.Explorer documentation built on Oct. 20, 2024, 8:20 p.m.