get_input: Get input data

In caravagnalab/basilica: bascule

Get input data

Description

Get input data

Usage

get_input(
  x,
  types = get_types(x),
  samples = get_samples(x),
  clusters = get_cluster_labels(x),
  matrix = FALSE,
  reconstructed = FALSE,
  add_groups = FALSE,
  by_sigs = FALSE
)

Arguments

x	bascule object.
types	List of variant types to subset
samples	List of samples to subset
clusters	List of clusters to subset
matrix	Logical. If 'TRUE', the output will be in wide format.
reconstructed	Logical. If 'TRUE', the reconstructed counts, i.e., computed as alpha x beta, will be returned.
add_groups	Logical. If 'TRUE' and clustering has been performed, each sample will be annotated with the assigned group.
by_sigs	Logical. If 'TRUE', the number of mutations generated by each signature will be returned.

Value

list of long or wide-formatted mutations counts.

caravagnalab/basilica documentation built on June 11, 2025, 10:18 p.m.