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Compute links between DNA regions and genenames

bipartite_peaks2genes.Rd

Compute and add bipartite between DNA regions and genenames to hummus object. Links are computed based on the distance between peaks and gene's TSS location from gene.range annotations. Call find_peaks_near_genes function, that can use different methods.

Usage

bipartite_peaks2genes(
  hummus_object,
  gene_assay = "RNA",
  peak_assay = "peaks",
  gene_multiplex_name = NULL,
  peak_multiplex_name = NULL,
  peak_to_gene_method = "Signac",
  upstream = 500,
  downstream = 500,
  only_tss = TRUE,
  store_network = FALSE,
  output_file = NULL,
  bipartite_name = "atac_rna"
)

Arguments

hummus_object

(hummus_object) - Hummus object.

gene_assay

(character) - Name of assay containing the gene expression data. Default: "RNA".

peak_assay

(character) - Name of the assay containing the DNA regions (ATAC peaks). Default: "peaks".

gene_multiplex_name

(character) - Name of the multiplex containing the genes. If NULL, the name of the gene assay is used.

peak_multiplex_name

(character) - Name of the multiplex containing the DNA regions (ATAC peaks). If NULL, the name of the peak assay is used.

peak_to_gene_method

(character) - Method to use to compute the links between peaks and genes. Default: "Signac".

  • 'Signac' - Use Signac::Extend to extend genes.

  • 'GREAT' - Not implemented yet.

upstream

(int) - Upstream distance from TSS to consider as potential promoter.

downstream

(int) - Downstream distance from TSS to consider as potential promoter.

only_tss

(logical) - If TRUE, only TSS will be considered.

store_network

(bool) - Save the bipartite directly (TRUE, default) or return without saving on disk (FALSE).

output_file

(character) - Name of the output_file (if store_bipartite == TRUE). Default: NULL.

bipartite_name

(character) - Name of bipartite. Default: "atac_rna".

verbose

(integer) Display function messages. Set to 0 for no message displayed, >= 1 for more details. Default: 1.

Value

hummus_object (hummus_object) - Hummus object w/ atac-rna bipartite added to the multilayer slot

Examples

hummus <- bipartite_peaks2genes(
                       hummus_object = hummus,
                       gene_assay = "RNA",
                       peak_assay = "peaks",
                       gene_multiplex_name = "RNA",
                       peak_multiplex_name = "peaks",
                       peak_to_gene_method = "Signac",
                       upstream = 500,
                       downstream = 500,
                       only_tss = TRUE,
                       store_network = FALSE,
                       bipartite_name = "atac_rna")
#> Error: object 'hummus' not found