Calculate wedge features from a kernel

Usage

calculateWedges(
  kernel,
  unifKernel = NULL,
  cells,
  Dcell = NULL,
  bundle = TRUE,
  patient_names = NULL,
  zero_threshold = 1
)

Arguments

kernel: Kernel array returned by compute_kernel().
unifKernel: Optional normalized baseline kernel.
cells: Character vector of cell-type names.
Dcell: Patient-by-cell-type abundance matrix, used to weight raw (unnormalized) scores. Ignored when unifKernel is supplied.
bundle: Logical; if TRUE, combine directionally equivalent wedges.
patient_names: Optional character vector of patient labels, matching the patient order in kernel. Defaults to Patient_1, Patient_2, ... when omitted.
zero_threshold: Drop a wedge once its fraction of zero-valued patients reaches this threshold. Default 1 only drops wedges that are zero for every patient (the original behavior); lower it (e.g. 0.9) to also drop merely zero-inflated wedges.

Value

A patient-by-feature data frame of wedge scores. Triplets with no possible ligand-receptor pathway in any patient (zero for every patient) are dropped rather than returned as all-zero columns.