run_numbat {numbat}

Run workflow to decompose tumor subclones

Description

Run workflow to decompose tumor subclones

Usage

run_numbat(
  count_mat,
  lambdas_ref,
  df_allele,
  genome = "hg38",
  out_dir = tempdir(),
  max_iter = 2,
  max_nni = 100,
  t = 1e-05,
  gamma = 20,
  min_LLR = 5,
  alpha = 1e-04,
  eps = 1e-05,
  max_entropy = 0.5,
  init_k = 3,
  min_cells = 50,
  tau = 0.3,
  nu = 1,
  max_cost = ncol(count_mat) * tau,
  n_cut = 0,
  min_depth = 0,
  common_diploid = TRUE,
  min_overlap = 0.45,
  ncores = 1,
  ncores_nni = ncores,
  random_init = FALSE,
  segs_loh = NULL,
  call_clonal_loh = FALSE,
  verbose = TRUE,
  diploid_chroms = NULL,
  segs_consensus_fix = NULL,
  use_loh = NULL,
  min_genes = 10,
  skip_nj = FALSE,
  multi_allelic = TRUE,
  p_multi = 1 - alpha,
  plot = TRUE,
  check_convergence = FALSE,
  exclude_neu = TRUE
)

Arguments

count_mat

dgCMatrix Raw count matrices where rownames are genes and column names are cells

lambdas_ref

matrix Either a named vector with gene names as names and normalized expression as values, or a matrix where rownames are genes and columns are pseudobulk names

df_allele

dataframe Allele counts per cell, produced by preprocess_allele

genome

character Genome version (hg38, hg19, or mm10)

out_dir

string Output directory

max_iter

integer Maximum number of iterations to run the phyologeny optimization

max_nni

integer Maximum number of iterations to run NNI in the ML phylogeny inference

t

numeric Transition probability

gamma

numeric Dispersion parameter for the Beta-Binomial allele model

min_LLR

numeric Minimum LLR to filter CNVs

alpha

numeric P value cutoff for diploid finding

eps

numeric Convergence threshold for ML tree search

max_entropy

numeric Entropy threshold to filter CNVs

init_k

integer Number of clusters in the initial clustering

min_cells

integer Minimum number of cells to run HMM on

tau

numeric Factor to determine max_cost as a function of the number of cells (0-1)

nu

numeric Phase switch rate

max_cost

numeric Likelihood threshold to collapse internal branches

n_cut

integer Number of cuts on the phylogeny to define subclones

min_depth

integer Minimum allele depth

common_diploid

logical Whether to find common diploid regions in a group of peusdobulks

min_overlap

numeric Minimum CNV overlap threshold

ncores

integer Number of threads to use

ncores_nni

integer Number of threads to use for NNI

random_init

logical Whether to initiate phylogney using a random tree (internal use only)

segs_loh

dataframe Segments of clonal LOH to be excluded

call_clonal_loh

logical Whether to call segments with clonal LOH

verbose

logical Verbosity

diploid_chroms

vector Known diploid chromosomes

segs_consensus_fix

dataframe Pre-determined segmentation of consensus CNVs

use_loh

logical Whether to include LOH regions in the expression baseline

min_genes

integer Minimum number of genes to call a segment

skip_nj

logical Whether to skip NJ tree construction and only use UPGMA

multi_allelic

logical Whether to call multi-allelic CNVs

p_multi

numeric P value cutoff for calling multi-allelic CNVs

plot

logical Whether to plot results

check_convergence

logical Whether to terminate iterations based on consensus CNV convergence

exclude_neu

logical Whether to exclude neutral segments from CNV retesting (internal use only)

Value

a status code