run_numbat: Run workflow to decompose tumor subclones
In whtns/numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

run_numbat

R Documentation

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,
  max_cost = ncol(count_mat) * tau,
  min_depth = 0,
  common_diploid = TRUE,
  min_overlap = 0.45,
  ncores = 1,
  ncores_nni = ncores,
  random_init = FALSE,
  segs_loh = NULL,
  verbose = TRUE,
  diploid_chroms = 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 or hg19)
`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)
`max_cost`	numeric Likelihood threshold to collapse internal branches
`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
`verbose`	logical Verbosity
`diploid_chroms`	vector Known diploid chromosomes
`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)