Get base GRN from Cicero/ATAC data

Processes Cicero coaccessibility results to create a base GRN. This connects peaks to genes based on proximity and coaccessibility.

Usage

get_base_grn_from_cicero(
  cicero_connections,
  peak_annotation,
  coaccess_threshold = 0.05,
  max_distance = 1e+05
)

Arguments

cicero_connections

Cicero connection data frame

peak_annotation

Peak-to-gene annotation data frame

coaccess_threshold

Coaccessibility score threshold

max_distance

Maximum distance for peak-gene association

Value

Data frame suitable for TFinfo import