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Annotate Regulatory Elements with Gene Targets Using Co-Accessibility Links

Source: R/annotate_re_genes.R
annotate_with_coaccessibility.Rd

This function annotates regulatory elements (REs) with their putative gene targets by integrating co-accessibility links that include CCAN (co-accessibility networks) metadata. It extracts promoter regions from a TxDb object, optionally filters for protein-coding genes, and links REs to genes based on chromatin co-accessibility. Optionally, REs overlapping a transcription start site (TSS) can also be annotated directly.

Usage

annotate_with_coaccessibility(
  links,
  retsi,
  txdb,
  annot_dbi,
  protein_coding_only = TRUE,
  keep_mito = FALSE,
  verbose = TRUE,
  coaccess_cutoff_override = 0.25,
  filter_promoter_distal = TRUE,
  add_tss_annotation = TRUE
)

Arguments

A GInteractions object representing co-accessibility links with CCAN metadata.

retsi

A GRanges or data.frame object representing regulatory elements to annotate. If a data.frame, must contain columns sufficient to construct GRanges (e.g., seqnames, start, end).

txdb

A TxDb object used to extract promoter regions and TSS annotations.

annot_dbi

An AnnotationDbi annotation database object (e.g., org.Hs.eg.db) for mapping gene IDs to gene symbols and types.

protein_coding_only

Logical indicating whether to restrict promoter regions to protein-coding genes only (default: TRUE).

keep_mito

Logical indicating whether to keep mitochondrial (chrM/MT) chromosomes in promoter extraction (default: FALSE).

verbose

Logical; if TRUE, informative messages are printed during processing (default: TRUE).

coaccess_cutoff_override

Numeric; co-accessibility score cutoff to override default filtering in annotate_links_with_ccans (default: 0.25).

filter_promoter_distal

Logical; whether to filter links to retain only promoter-distal interactions (default: TRUE).

add_tss_annotation

Logical; whether to annotate regulatory elements overlapping TSS directly (default: TRUE).

Value

A data.frame with regulatory elements annotated with:

  • Distance to nearest TSS and promoter/distal classification

  • Co-accessible gene targets

  • Optional: TSS overlap and TSS gene symbol