Run workflow to decompose tumor subclones
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
)a status code
dgCMatrix Raw count matrices where rownames are genes and column names are cells
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
dataframe Allele counts per cell, produced by preprocess_allele
character Genome version (hg38, hg19, or mm10)
string Output directory
integer Maximum number of iterations to run the phyologeny optimization
integer Maximum number of iterations to run NNI in the ML phylogeny inference
numeric Transition probability
numeric Dispersion parameter for the Beta-Binomial allele model
numeric Minimum LLR to filter CNVs
numeric P value cutoff for diploid finding
numeric Convergence threshold for ML tree search
numeric Entropy threshold to filter CNVs
integer Number of clusters in the initial clustering
integer Minimum number of cells to run HMM on
numeric Factor to determine max_cost as a function of the number of cells (0-1)
numeric Phase switch rate
numeric Likelihood threshold to collapse internal branches
integer Number of cuts on the phylogeny to define subclones
integer Minimum allele depth
logical Whether to find common diploid regions in a group of peusdobulks
numeric Minimum CNV overlap threshold
integer Number of threads to use
integer Number of threads to use for NNI
logical Whether to initiate phylogney using a random tree (internal use only)
dataframe Segments of clonal LOH to be excluded
logical Whether to call segments with clonal LOH
logical Verbosity
vector Known diploid chromosomes
dataframe Pre-determined segmentation of consensus CNVs
logical Whether to include LOH regions in the expression baseline
integer Minimum number of genes to call a segment
logical Whether to skip NJ tree construction and only use UPGMA
logical Whether to call multi-allelic CNVs
numeric P value cutoff for calling multi-allelic CNVs
logical Whether to plot results
logical Whether to terminate iterations based on consensus CNV convergence
logical Whether to exclude neutral segments from CNV retesting (internal use only)