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Compute links between TFs and DNA regions (ATAC peaks)

bipartite_tfs2peaks.Rd

Compute and add bipartite between TFs and DNA regions to hummus object. Links are computed based on the binding motifs of TFs and their locations on a reference genome. Currently based on Signac AddMotifs function (–> motifmachR, itself based on MOODs algorithm).

Usage

bipartite_tfs2peaks(
  hummus_object,
  tf_expr_assay = "RNA",
  peak_assay = "peaks",
  tf_multiplex_name = NULL,
  peak_multiplex_name = NULL,
  genome,
  store_network = FALSE,
  output_file = NULL,
  verbose = 1,
  bipartite_name = "tf_peak"
)

Arguments

hummus_object

(hummus_object) - Hummus object.

tf_expr_assay

(character) - Name of assay containing the TF expression data. If NULL, all TFs with a motif are used. Default: "RNA".

peak_assay

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

tf_multiplex_name

(character) - Name of multiplex containing the TFs. If NULL, the name of the TF 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.

genome

(BSgenome object) - Reference genome.

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.

verbose

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

bipartite_name

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

Value

hummus_object (hummus_object) - Hummus object with TF-peak bipartite added to the multilayer slot

Examples

hummus <- bipartite_tfs2peaks(
                     hummus_object = hummus,
                     tf_expr_assay = "RNA",
                     peak_assay = "peaks",
                     tf_multiplex_name = "TF",
                     peak_multiplex_name = "peaks",
          genome = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
                     store_network = FALSE,
                     verbose = 1,
                     bipartite_name = "tf_peak")
#> Computing TF-peak bipartite
#> Error: object 'hummus' not found