This function runs the SPICEY pipeline to compute tissue specificity scores from single-cell ATAC-seq (RETSI) and/or RNA-seq (GETSI) data. It optionally links regulatory elements to genes using either nearest-gene or co-accessibility based annotation, and can combine RETSI and GETSI values for downstream integration.
Usage
run_spicey(
atac = NULL,
rna = NULL,
annot_method = NULL,
links = NULL,
link_spicey_measures = FALSE,
coaccess_cutoff_override = 0.25,
filter_promoter_distal = TRUE,
filter_protein_coding = TRUE,
txdb = NULL,
keep_mito = FALSE,
annot_dbi = NULL,
add_tss_annotation = FALSE,
verbose = TRUE
)Arguments
- atac
A Seurat or SummarizedExperiment object containing scATAC-seq data.
- rna
A Seurat or SummarizedExperiment object containing scRNA-seq data.
- annot_method
Method for region-to-gene annotation: "nearest" or "coaccessibility".
- links
Co-accessibility links (e.g., from Cicero or ArchR) for co-accessibility annotation.
- link_spicey_measures
Logical; whether to link RETSI and GETSI via annotated genes.
- coaccess_cutoff_override
Minimum co-accessibility score to retain links (default: 0.25).
- filter_promoter_distal
Logical; whether to exclude promoter-proximal links (default: TRUE).
- filter_protein_coding
Logical; whether to filter to protein-coding genes only (default: TRUE).
- txdb
A TxDb object for genomic annotations.
- keep_mito
Logical; whether to keep mitochondrial regions (default: FALSE).
- annot_dbi
Optional AnnotationDbi object for additional gene info (e.g., gene symbols).
- add_tss_annotation
Logical; whether to include TSS annotation columns in the output (default: FALSE).
- verbose
Logical; whether to print messages during execution (default: TRUE).