Package {scShardSplitRef}

Title:	Build Custom Reference Genome for Single-Cell Multiome ATAC and Gene Expression Data of Large-Genome Species
Version:	0.1.0
Description:	Provides utilities that enable researchers to build custom references for the Multiome ATAC Gene Expression sequencing data for large-genome species without manual intervention.
License:	GPL (≥ 3)
Depends:	R (≥ 4.3.0)
Imports:	cli, rlang, stringi, utils, withr
Suggests:	knitr, rmarkdown, roxyglobals, testthat (≥ 3.0.0)
VignetteBuilder:	knitr
Config/testthat/edition:	3
Encoding:	UTF-8
Config/roxyglobals/filename:	globals.R
Config/roxyglobals/unique:	FALSE
Config/roxygen2/version:	8.0.0
Config/Needs/build:	moodymudskipper/devtag
NeedsCompilation:	no
Packaged:	2026-07-15 03:01:12 UTC; ikrstudio
Author:	Irina Kuznetsova [aut, cre], Luke Pembleton [aut], Luca Curci [aut], Adam H. Sparks [aut], Curtin University [fnd, cph], Grains Research and Development Corporation [fnd, cph] (GRDC Project CUR2210-005OPX (AAGI-CU))
Maintainer:	Irina Kuznetsova <irina.kuznetsova@curtin.edu.au>
Repository:	CRAN
Date/Publication:	2026-07-23 12:30:02 UTC

scShardSplitRef: Build Custom Reference Genome for Single-Cell Multiome ATAC and Gene Expression Data of Large-Genome Species

Description

Provides utilities that enable researchers to build custom references for the Multiome ATAC Gene Expression sequencing data for large-genome species without manual intervention.

Author(s)

Maintainer: Irina Kuznetsova irina.kuznetsova@curtin.edu.au (ORCID)

Authors:

• Irina Kuznetsova irina.kuznetsova@curtin.edu.au (ORCID)

• Luke Pembleton lpembleton@barenbrug.com.au (ORCID)

• Luca Curci pasqualeluca.curci@cnr.it (ORCID)

• Adam H. Sparks adamhsparks@gmail.com (ORCID)

Other contributors:

• Curtin University (ROR) [funder, copyright holder]

• Grains Research and Development Corporation (ROR) (GRDC Project CUR2210-005OPX (AAGI-CU)) [funder, copyright holder]

Determine split regions for reference sharding

Description

Builds BED-like split intervals from genomic regions and GTF gene annotations. If the start position in a genomic region is not 0, it is assumed to mark the start of a centromere and the region is split around that point. Proposed boundaries are shifted rightward when they fall too close to gene intervals, and oversized chunks are repeatedly re-split until all segments satisfy the requested size limit.

Usage

determine_split_regions(
  bed,
  gtf,
  output_bed,
  limit = 2L^29L,
  shift_by = 1L,
  clearance = 1L
)

Arguments

Details

The function performs the following steps:

1. Reads genomic regions and gene annotations from input files.

2. Checks that the provided limit is feasible given gene positions and requested two-sided boundary clearance.

3. For each region, splits it at the centromere (if start > 0) and applies the size limit.

4. Adjusts boundaries so each is at least clearance bp away from genes on both sides, moving by shift_by bp per iteration when needed.

5. Iteratively subdivides intervals exceeding the limit until all intervals satisfy the constraint.

6. Writes final split regions to BED file in the active R session's tempdir().

Value

Invisible character: path to the written BED file.

Examples

  # load example files from this package and write the output bed file to
  # R's tempdir()

  chromosomes <- system.file("extdata",
                   "AlgorithmToy.bed",
                   package = "scShardSplitRef",
                   mustWork = TRUE)
  genes <- system.file("extdata",
             "AlgorithmToy.gtf",
             package = "scShardSplitRef",
             mustWork = TRUE)

  determine_split_regions(
    bed = chromosomes,
    gtf = genes,
    output_bed = file.path(tempdir(), "split_regions.bed"),
    limit = 2L^29L,
    shift_by = 1L,
    clearance = 1L
  )

Process a GTF file by assigning split-region sequence names

Description

Reads a BED-like "split regions" file and a GTF, assigns each GTF feature to exactly one split-region interval, and replaces the GTF Chr field with a split-region name of the form Chr-RegionStart-RegionEnd.

Usage

process_gtf(
  split_regions_bed,
  gtf,
  genome_name,
  genome_version = NULL,
  keep_attributes = NULL,
  out_path = "."
)

Arguments

Details

A feature is considered inside a region when:

• start >= RegionStart

• start < RegionEnd

• end <= RegionEnd

The function aborts if:

• any GTF feature matches more than one region (overlapping regions), or

• any GTF feature matches no region (regions don't fully cover the GTF).

Value

The function writes the filtered GTF file to disk.

Output file

The function will automatically name the file based on the input file and prepends the following string onto the filename: "B1_FINAL_MODIFIED_GTF_genome_name_genome_version.gtf", placing the file in the directory specified in the out_path.

Examples

reg_file <- system.file(
  "extdata/AlgorithmToy_DetermineSplitReg.bed",
  package = "scShardSplitRef",
  mustWork = TRUE
)
gtf_file <- system.file(
  "extdata/AlgorithmToy.gtf",
  package = "scShardSplitRef",
  mustWork = TRUE
)

process_gtf(
  split_regions_bed = reg_file,
  gtf = gtf_file,
  genome_name = "Example",
  genome_version = "v1.0",
  out_path = tempdir()
)

Get or Set scShardSplitRef Options

Description

A convenience function to get or set options used by scShardSplitRef.

Usage

scShardSplitRef_options(...)

Arguments

Value

A list of current option values.

Examples

# See currently set options for scShardSplitRef
scShardSplitRef_options()

# Set verbose to FALSE to suppress info/success messages
scShardSplitRef_options(scShardSplitRef.verbose = FALSE)
scShardSplitRef_options()