Reads an ATAC object from an h5ad file. Peak data is taken from the 'X' section and metadata is taken from 'obs'. The 'var' section can contain a special field called 'ignore' which marks peaks that should be ignored.
Usage
import_from_h5ad(
file,
class = NULL,
genome = NULL,
id = NULL,
description = NULL,
tad_based = NULL
)Arguments
- file
name of an h5ad file with ATAC data
- class
is the file storing ScPeaks or McPeaks. If NULL - the class would be determined by the 'class' field in the 'uns' part of the h5ad file, if exists and otherwise the class would be McPeaks.
- genome
genome assembly of the peaks. e.g. "hg38", "hg19", "mm9", "mm10". If NULL - the assembly would be determined by the 'genome' field in the 'uns' part of the h5ad file.
- id
an identifier for the object, e.g. "pbmc". If NULL - the id would be determined by the 'id' field in the 'uns' part of the h5ad file, and if this doesn't exist - a random id would be assigned.
- description
description of the object, e.g. "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)". If NULL - the id would be determined by the 'description' field in the 'uns' part of the h5ad file
- tad_based
whether to name peaks based on TADs if possible (when an intervals set named "intervs.global.tad_names" exists). When FALSE - peaks are named based on their coordinates. if NULL - the value would be determined by the 'tad_based' field in the 'uns' part of the h5ad file, and if this doesn't exist - the value would be TRUE.
Examples
if (FALSE) {
atac_sc <- import_from_10x("pbmc_data", genome = "hg38")
export_to_h5ad(atac_sc, "pbmc_data/atac_sc.h5ad")
atac_sc_loaded <- import_from_h5ad("pbmc_data/atac_sc.h5ad")
}